clang-tidy-errors

/home/benj/projects/tskit/c/build/../tskit/convert.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/convert.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/core.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/core.c:77:37: warning: use 'fopen' mode 'e' to set O_CLOEXEC [android-cloexec-fopen]
    FILE *f = fopen("/dev/urandom", "r");
                                    ^~~~
                                    "re"
/home/benj/projects/tskit/c/build/../tskit/core.c:430:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return err ^ (1 << TSK_KAS_ERR_BIT);
           ^
/home/benj/projects/tskit/c/build/../tskit/core.c:430:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return err ^ (1 << TSK_KAS_ERR_BIT);
                  ^
/home/benj/projects/tskit/c/build/../tskit/core.c:436:14: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !(err & (1 << TSK_KAS_ERR_BIT));
             ^
/home/benj/projects/tskit/c/build/../tskit/core.c:436:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !(err & (1 << TSK_KAS_ERR_BIT));
                    ^
/home/benj/projects/tskit/c/build/../tskit/core.c:443:17: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        err ^= (1 << TSK_KAS_ERR_BIT);
                ^
/home/benj/projects/tskit/c/build/../tskit/core.c:445:7: warning: do not use 'else' after 'return' [readability-else-after-return]
    } else {
      ^~~~~~
../tskit/core.h:309:5: warning: function 'tsk_generate_uuid' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_generate_uuid(char *dest, int flags);
    ^
/home/benj/projects/tskit/c/build/../tskit/core.c:100:1: note: the definition seen here
tsk_generate_uuid(char *dest, int TSK_UNUSED(flags))
^
../tskit/core.h:309:5: note: differing parameters are named here: ('flags'), in definition: ('TSK_UNUSED_flags')
int tsk_generate_uuid(char *dest, int flags);
    ^
/home/benj/projects/tskit/c/build/../tskit/core.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/core.c:77:37: warning: use 'fopen' mode 'e' to set O_CLOEXEC [android-cloexec-fopen]
    FILE *f = fopen("/dev/urandom", "r");
                                    ^~~~
                                    "re"
/home/benj/projects/tskit/c/build/../tskit/core.c:430:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return err ^ (1 << TSK_KAS_ERR_BIT);
           ^
/home/benj/projects/tskit/c/build/../tskit/core.c:430:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return err ^ (1 << TSK_KAS_ERR_BIT);
                  ^
/home/benj/projects/tskit/c/build/../tskit/core.c:436:14: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !(err & (1 << TSK_KAS_ERR_BIT));
             ^
/home/benj/projects/tskit/c/build/../tskit/core.c:436:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !(err & (1 << TSK_KAS_ERR_BIT));
                    ^
/home/benj/projects/tskit/c/build/../tskit/core.c:443:17: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        err ^= (1 << TSK_KAS_ERR_BIT);
                ^
/home/benj/projects/tskit/c/build/../tskit/core.c:445:7: warning: do not use 'else' after 'return' [readability-else-after-return]
    } else {
      ^~~~~~
../tskit/core.h:309:5: warning: function 'tsk_generate_uuid' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_generate_uuid(char *dest, int flags);
    ^
/home/benj/projects/tskit/c/build/../tskit/core.c:100:1: note: the definition seen here
tsk_generate_uuid(char *dest, int TSK_UNUSED(flags))
^
../tskit/core.h:309:5: note: differing parameters are named here: ('flags'), in definition: ('TSK_UNUSED_flags')
int tsk_generate_uuid(char *dest, int flags);
    ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:87:30: warning: Result of 'malloc' is converted to a pointer of type 'char', which is incompatible with sizeof operand type 'char *' [clang-analyzer-unix.MallocSizeof]
    self->user_alleles_mem = malloc(total_len * sizeof(char *));
                             ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:87:30: note: Result of 'malloc' is converted to a pointer of type 'char', which is incompatible with sizeof operand type 'char *'
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:94:9: warning: Call to function 'strcpy' is insecure as it does not provide bounding of the memory buffer. Replace unbounded copy functions with analogous functions that support length arguments such as 'strlcpy'. CWE-119 [clang-analyzer-security.insecureAPI.strcpy]
        strcpy(self->user_alleles_mem + offset, alleles[j]);
        ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:94:9: note: Call to function 'strcpy' is insecure as it does not provide bounding of the memory buffer. Replace unbounded copy functions with analogous functions that support length arguments such as 'strlcpy'. CWE-119
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:110:30: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool impute_missing = !!(options & TSK_IMPUTE_MISSING_DATA);
                             ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:110:40: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool impute_missing = !!(options & TSK_IMPUTE_MISSING_DATA);
                                       ^
../tskit/genotypes.h:36:34: note: expanded from macro 'TSK_IMPUTE_MISSING_DATA'
#define TSK_IMPUTE_MISSING_DATA (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:160:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_16_BIT_GENOTYPES) {
        ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:160:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_16_BIT_GENOTYPES) {
                        ^
../tskit/genotypes.h:35:31: note: expanded from macro 'TSK_16_BIT_GENOTYPES'
#define TSK_16_BIT_GENOTYPES (1 << 0)
                              ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:176:75: warning: statement should be inside braces [hicpp-braces-around-statements]
        for (max_alleles = 0; alleles[max_alleles] != NULL; max_alleles++)
                                                                          ^
                                                                           {
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:208:24: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        tree_options = TSK_SAMPLE_LISTS;
                       ^
../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:248:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_16_BIT_GENOTYPES) {
        ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:248:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_16_BIT_GENOTYPES) {
                        ^
../tskit/genotypes.h:35:31: note: expanded from macro 'TSK_16_BIT_GENOTYPES'
#define TSK_16_BIT_GENOTYPES (1 << 0)
                              ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:497:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool genotypes16 = !!(self->options & TSK_16_BIT_GENOTYPES);
                          ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:497:43: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool genotypes16 = !!(self->options & TSK_16_BIT_GENOTYPES);
                                          ^
../tskit/genotypes.h:35:31: note: expanded from macro 'TSK_16_BIT_GENOTYPES'
#define TSK_16_BIT_GENOTYPES (1 << 0)
                              ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:498:30: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool impute_missing = !!(self->options & TSK_IMPUTE_MISSING_DATA);
                             ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:498:46: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool impute_missing = !!(self->options & TSK_IMPUTE_MISSING_DATA);
                                             ^
../tskit/genotypes.h:36:34: note: expanded from macro 'TSK_IMPUTE_MISSING_DATA'
#define TSK_IMPUTE_MISSING_DATA (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:87:30: warning: Result of 'malloc' is converted to a pointer of type 'char', which is incompatible with sizeof operand type 'char *' [clang-analyzer-unix.MallocSizeof]
    self->user_alleles_mem = malloc(total_len * sizeof(char *));
                             ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:87:30: note: Result of 'malloc' is converted to a pointer of type 'char', which is incompatible with sizeof operand type 'char *'
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:94:9: warning: Call to function 'strcpy' is insecure as it does not provide bounding of the memory buffer. Replace unbounded copy functions with analogous functions that support length arguments such as 'strlcpy'. CWE-119 [clang-analyzer-security.insecureAPI.strcpy]
        strcpy(self->user_alleles_mem + offset, alleles[j]);
        ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:94:9: note: Call to function 'strcpy' is insecure as it does not provide bounding of the memory buffer. Replace unbounded copy functions with analogous functions that support length arguments such as 'strlcpy'. CWE-119
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:110:30: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool impute_missing = !!(options & TSK_IMPUTE_MISSING_DATA);
                             ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:110:40: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool impute_missing = !!(options & TSK_IMPUTE_MISSING_DATA);
                                       ^
../tskit/genotypes.h:36:34: note: expanded from macro 'TSK_IMPUTE_MISSING_DATA'
#define TSK_IMPUTE_MISSING_DATA (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:160:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_16_BIT_GENOTYPES) {
        ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:160:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_16_BIT_GENOTYPES) {
                        ^
../tskit/genotypes.h:35:31: note: expanded from macro 'TSK_16_BIT_GENOTYPES'
#define TSK_16_BIT_GENOTYPES (1 << 0)
                              ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:176:75: warning: statement should be inside braces [hicpp-braces-around-statements]
        for (max_alleles = 0; alleles[max_alleles] != NULL; max_alleles++)
                                                                          ^
                                                                           {
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:208:24: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        tree_options = TSK_SAMPLE_LISTS;
                       ^
../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:248:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_16_BIT_GENOTYPES) {
        ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:248:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_16_BIT_GENOTYPES) {
                        ^
../tskit/genotypes.h:35:31: note: expanded from macro 'TSK_16_BIT_GENOTYPES'
#define TSK_16_BIT_GENOTYPES (1 << 0)
                              ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:497:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool genotypes16 = !!(self->options & TSK_16_BIT_GENOTYPES);
                          ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:497:43: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool genotypes16 = !!(self->options & TSK_16_BIT_GENOTYPES);
                                          ^
../tskit/genotypes.h:35:31: note: expanded from macro 'TSK_16_BIT_GENOTYPES'
#define TSK_16_BIT_GENOTYPES (1 << 0)
                              ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:498:30: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool impute_missing = !!(self->options & TSK_IMPUTE_MISSING_DATA);
                             ^
/home/benj/projects/tskit/c/build/../tskit/genotypes.c:498:46: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool impute_missing = !!(self->options & TSK_IMPUTE_MISSING_DATA);
                                             ^
../tskit/genotypes.h:36:34: note: expanded from macro 'TSK_IMPUTE_MISSING_DATA'
#define TSK_IMPUTE_MISSING_DATA (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:25:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:120:13: warning: pointer parameter 'recombination_rate' can be pointer to const [readability-non-const-parameter]
    double *recombination_rate, double *mutation_rate, tsk_flags_t options)
    ~~~~~~  ^
    const 
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:120:41: warning: pointer parameter 'mutation_rate' can be pointer to const [readability-non-const-parameter]
    double *recombination_rate, double *mutation_rate, tsk_flags_t options)
                                ~~~~~~  ^
                                const 
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:171:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (options & TSK_ALLELES_ACGT) {
            ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:171:23: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (options & TSK_ALLELES_ACGT) {
                      ^
../tskit/haplotype_matching.h:36:27: note: expanded from macro 'TSK_ALLELES_ACGT'
#define TSK_ALLELES_ACGT (1 << 16)
                          ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:531:19: warning: redundant cast to the same type [google-readability-casting]
    size_t base = (size_t) u * num_words;
                  ^~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:551:7: warning: do not use 'else' after 'return' [readability-else-after-return]
    } else {
      ^~~~~~
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:559:21: warning: redundant cast to the same type [google-readability-casting]
    size_t index = ((size_t) u) * num_words + (size_t)(state / 64);
                    ^~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:560:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return (A[index] & (1ULL << (state % 64))) != 0;
                        ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:567:17: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    A[index] |= 1ULL << (state % 64);
                ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:584:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            child = 1ULL << parent_state;
                    ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:604:33: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const uint64_t state_word = 1ULL << (parent_state % 64);
                                ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:641:33: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const uint64_t state_word = 1ULL << (parent_state % 64);
                                ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:906:36: warning: redundant cast to the same type [google-readability-casting]
    const unsigned int precision = (unsigned int) self->precision;
                                   ^~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1044:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1126:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1177:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        block_size = 1 << 20;
                     ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1315:53: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_tree_init(&tree, self->tree_sequence, TSK_SAMPLE_LISTS);
                                                    ^
../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1376:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        block_size = 1 << 20; /* 1MiB */
                     ^
../tskit/haplotype_matching.h:163:5: warning: function 'tsk_viterbi_matrix_traceback' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_viterbi_matrix_traceback(
    ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1510:1: note: the definition seen here
tsk_viterbi_matrix_traceback(
^
../tskit/haplotype_matching.h:163:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_viterbi_matrix_traceback(
    ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:25:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:120:13: warning: pointer parameter 'recombination_rate' can be pointer to const [readability-non-const-parameter]
    double *recombination_rate, double *mutation_rate, tsk_flags_t options)
    ~~~~~~  ^
    const 
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:120:41: warning: pointer parameter 'mutation_rate' can be pointer to const [readability-non-const-parameter]
    double *recombination_rate, double *mutation_rate, tsk_flags_t options)
                                ~~~~~~  ^
                                const 
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:171:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (options & TSK_ALLELES_ACGT) {
            ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:171:23: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (options & TSK_ALLELES_ACGT) {
                      ^
../tskit/haplotype_matching.h:36:27: note: expanded from macro 'TSK_ALLELES_ACGT'
#define TSK_ALLELES_ACGT (1 << 16)
                          ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:531:19: warning: redundant cast to the same type [google-readability-casting]
    size_t base = (size_t) u * num_words;
                  ^~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:551:7: warning: do not use 'else' after 'return' [readability-else-after-return]
    } else {
      ^~~~~~
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:559:21: warning: redundant cast to the same type [google-readability-casting]
    size_t index = ((size_t) u) * num_words + (size_t)(state / 64);
                    ^~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:560:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return (A[index] & (1ULL << (state % 64))) != 0;
                        ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:567:17: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    A[index] |= 1ULL << (state % 64);
                ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:584:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            child = 1ULL << parent_state;
                    ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:604:33: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const uint64_t state_word = 1ULL << (parent_state % 64);
                                ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:641:33: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const uint64_t state_word = 1ULL << (parent_state % 64);
                                ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:906:36: warning: redundant cast to the same type [google-readability-casting]
    const unsigned int precision = (unsigned int) self->precision;
                                   ^~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1044:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1126:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1177:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        block_size = 1 << 20;
                     ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1315:53: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_tree_init(&tree, self->tree_sequence, TSK_SAMPLE_LISTS);
                                                    ^
../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1376:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        block_size = 1 << 20; /* 1MiB */
                     ^
../tskit/haplotype_matching.h:163:5: warning: function 'tsk_viterbi_matrix_traceback' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_viterbi_matrix_traceback(
    ^
/home/benj/projects/tskit/c/build/../tskit/haplotype_matching.c:1510:1: note: the definition seen here
tsk_viterbi_matrix_traceback(
^
../tskit/haplotype_matching.h:163:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_viterbi_matrix_traceback(
    ^
/home/benj/projects/tskit/c/build/../tskit/stats.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/stats.c:81:64: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_tree_init(self->outer_tree, self->tree_sequence, TSK_SAMPLE_LISTS);
                                                               ^
../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/stats.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/stats.c:81:64: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_tree_init(self->outer_tree, self->tree_sequence, TSK_SAMPLE_LISTS);
                                                               ^
../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/tables.c:117:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        } else if (!(read_cols[j].options & TSK_COL_OPTIONAL)) {
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:117:45: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        } else if (!(read_cols[j].options & TSK_COL_OPTIONAL)) {
                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:146:44: warning: pointer parameter 'offsets' can be pointer to const [readability-non-const-parameter]
check_offsets(size_t num_rows, tsk_size_t *offsets, tsk_size_t length, bool check_length)
                               ~~~~~~~~~~  ^
                               const 
/home/benj/projects/tskit/c/build/../tskit/tables.c:295:32: warning: redundant cast to the same type [google-readability-casting]
    self->max_rows_increment = (tsk_size_t) max_rows_increment;
                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:306:43: warning: redundant cast to the same type [google-readability-casting]
    self->max_metadata_length_increment = (tsk_size_t) max_metadata_length_increment;
                                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:317:43: warning: redundant cast to the same type [google-readability-casting]
    self->max_location_length_increment = (tsk_size_t) max_location_length_increment;
                                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:360:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:414:58: warning: redundant cast to the same type [google-readability-casting]
    ret = tsk_individual_table_expand_main_columns(self, (tsk_size_t) num_rows);
                                                         ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:422:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->location_length;
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:431:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->location_length + location_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:445:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length;
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:454:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length + metadata_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:465:23: warning: redundant cast to the same type [google-readability-casting]
    self->num_rows += (tsk_size_t) num_rows;
                      ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:504:54: warning: redundant cast to the same type [google-readability-casting]
    ret = tsk_individual_table_expand_location(self, (tsk_size_t) location_length);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:508:54: warning: redundant cast to the same type [google-readability-casting]
    ret = tsk_individual_table_expand_metadata(self, (tsk_size_t) metadata_length);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:513:9: warning: redundant cast to the same type [google-readability-casting]
        (tsk_size_t) location_length, metadata, (tsk_size_t) metadata_length);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:513:49: warning: redundant cast to the same type [google-readability-casting]
        (tsk_size_t) location_length, metadata, (tsk_size_t) metadata_length);
                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:600:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:747:52: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            &metadata_schema_length, 0, KAS_UINT8, TSK_COL_OPTIONAL },
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:897:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:964:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length + metadata_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:989:23: warning: redundant cast to the same type [google-readability-casting]
    self->num_rows += (tsk_size_t) num_rows;
                      ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1184:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1236:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            0, KAS_UINT8, TSK_COL_OPTIONAL },
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1396:5: warning: Null pointer passed as an argument to a 'nonnull' parameter [clang-analyzer-core.NonNullParamChecker]
    memcpy(self->metadata + self->metadata_length, metadata, metadata_length);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5974:5: note: Loop condition is false. Execution continues on line 5991
    for (j = start; j < end; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5991:11: note: Calling 'simplifier_merge_ancestors'
    ret = simplifier_merge_ancestors(self, parent);
          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5865:22: note: Assuming the condition is false
    bool is_sample = output_id != TSK_NULL;
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5866:24: note: Assuming the condition is false
    bool keep_unary = !!(self->options & TSK_KEEP_UNARY);
                       ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5868:5: note: Taking false branch
    if (is_sample) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5878:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5882:12: note: Assuming the condition is true
    while ((ret = segment_overlapper_next(
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5882:5: note: Loop condition is true.  Entering loop body
    while ((ret = segment_overlapper_next(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5887:13: note: Assuming 'num_overlapping' is not equal to 1
        if (num_overlapping == 1) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5887:9: note: Taking false branch
        if (num_overlapping == 1) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5905:13: note: Taking true branch
            if (output_id == TSK_NULL) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5907:17: note: Taking false branch
                if (ret < 0) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5913:13: note: Loop condition is true.  Entering loop body
            for (j = 0; j < num_overlapping; j++) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5915:17: note: Taking false branch
                if (ret != 0) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5913:13: note: Loop condition is true.  Entering loop body
            for (j = 0; j < num_overlapping; j++) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5915:17: note: Taking false branch
                if (ret != 0) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5913:25: note: Assuming 'j' is >= 'num_overlapping'
            for (j = 0; j < num_overlapping; j++) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5913:13: note: Loop condition is false. Execution continues on line 5920
            for (j = 0; j < num_overlapping; j++) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5920:23: note: Left side of '&&' is false
        if (is_sample && left != prev_right) {
                      ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5927:9: note: Taking true branch
        if (keep_unary) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5931:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5882:12: note: Assuming the condition is false
    while ((ret = segment_overlapper_next(
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5882:5: note: Loop condition is false. Execution continues on line 5937
    while ((ret = segment_overlapper_next(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5937:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5937:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5940:19: note: Left side of '&&' is false
    if (is_sample && prev_right != self->tables->sequence_length) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5948:9: note: Assuming the condition is true
    if (output_id != TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5948:5: note: Taking true branch
    if (output_id != TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5949:15: note: Calling 'simplifier_flush_edges'
        ret = simplifier_flush_edges(self, output_id, &num_flushed_edges);
              ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5479:17: note: Assuming the condition is true
    for (j = 0; j < self->num_buffered_children; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5479:5: note: Loop condition is true.  Entering loop body
    for (j = 0; j < self->num_buffered_children; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5481:52: note: Assuming 'x' is equal to NULL
        for (x = self->child_edge_map_head[child]; x != NULL; x = x->next) {
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5481:9: note: Loop condition is false. Execution continues on line 5489
        for (x = self->child_edge_map_head[child]; x != NULL; x = x->next) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5479:17: note: Assuming the condition is true
    for (j = 0; j < self->num_buffered_children; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5479:5: note: Loop condition is true.  Entering loop body
    for (j = 0; j < self->num_buffered_children; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5481:52: note: Assuming 'x' is not equal to NULL
        for (x = self->child_edge_map_head[child]; x != NULL; x = x->next) {
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5481:9: note: Loop condition is true.  Entering loop body
        for (x = self->child_edge_map_head[child]; x != NULL; x = x->next) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5483:73: note: Passing null pointer value via 6th parameter 'metadata'
                &self->tables->edges, x->left, x->right, parent, child, NULL, 0);
                                                                        ^
/usr/lib/llvm-6.0/bin/../lib/clang/6.0.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5482:19: note: Calling 'tsk_edge_table_add_row'
            ret = tsk_edge_table_add_row(
                  ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1386:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1390:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1396:5: note: Null pointer passed as an argument to a 'nonnull' parameter
    memcpy(self->metadata + self->metadata_length, metadata, metadata_length);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1415:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1485:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length + metadata_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1634:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1683:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            TSK_COL_OPTIONAL },
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1685:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            TSK_COL_OPTIONAL },
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1687:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            0, KAS_UINT8, TSK_COL_OPTIONAL },
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1927:30: warning: redundant cast to the same type [google-readability-casting]
    ancestral_state_offset = (tsk_size_t) self->ancestral_state_length;
                             ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1938:23: warning: redundant cast to the same type [google-readability-casting]
    metadata_offset = (tsk_size_t) self->metadata_length;
                      ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:2032:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2164:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:2269:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            0, KAS_UINT8, TSK_COL_OPTIONAL },
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2365:42: warning: redundant cast to the same type [google-readability-casting]
        self->max_derived_state_length = (tsk_size_t) new_size;
                                         ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:2590:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2729:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:2839:52: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            &metadata_schema_length, 0, KAS_UINT8, TSK_COL_OPTIONAL },
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3036:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length + metadata_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:3060:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3192:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:3324:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            TSK_COL_OPTIONAL },
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3326:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            KAS_UINT32, TSK_COL_OPTIONAL },
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3328:52: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            &metadata_schema_length, 0, KAS_UINT8, TSK_COL_OPTIONAL },
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3465:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3639:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:3742:52: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            &metadata_schema_length, 0, KAS_UINT8, TSK_COL_OPTIONAL },
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3919:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:4127:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:4329:56: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_table_collection_check_integrity(tables, TSK_CHECK_OFFSETS);
                                                       ^
../tskit/tables.h:634:28: note: expanded from macro 'TSK_CHECK_OFFSETS'
#define TSK_CHECK_OFFSETS (1 << 0)
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:4940:67: warning: pointer parameter 'ancestors' can be pointer to const [readability-non-const-parameter]
ancestor_mapper_init_ancestors(ancestor_mapper_t *self, tsk_id_t *ancestors)
                                                        ~~~~~~~~  ^
                                                        const 
/home/benj/projects/tskit/c/build/../tskit/tables.c:5336:54: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        out, "\tfilter_unreferenced_sites: %d\n", !!(self->options & TSK_FILTER_SITES));
                                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5336:70: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        out, "\tfilter_unreferenced_sites: %d\n", !!(self->options & TSK_FILTER_SITES));
                                                                     ^
../tskit/tables.h:627:27: note: expanded from macro 'TSK_FILTER_SITES'
#define TSK_FILTER_SITES (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5338:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        !!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY));
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5338:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        !!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY));
                           ^
../tskit/tables.h:630:38: note: expanded from macro 'TSK_REDUCE_TO_SITE_TOPOLOGY'
#define TSK_REDUCE_TO_SITE_TOPOLOGY (1 << 3)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5339:45: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    fprintf(out, "\tkeep_unary  : %d\n", !!(self->options & TSK_KEEP_UNARY));
                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5339:61: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    fprintf(out, "\tkeep_unary  : %d\n", !!(self->options & TSK_KEEP_UNARY));
                                                            ^
../tskit/tables.h:631:25: note: expanded from macro 'TSK_KEEP_UNARY'
#define TSK_KEEP_UNARY (1 << 4)
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5393:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5393:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
                           ^
../tskit/tables.h:630:38: note: expanded from macro 'TSK_REDUCE_TO_SITE_TOPOLOGY'
#define TSK_REDUCE_TO_SITE_TOPOLOGY (1 << 3)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5444:61: warning: redundant cast to the same type [google-readability-casting]
    ret = tsk_node_table_get_row(&self->input_tables.nodes, (tsk_id_t) input_id, &node);
                                                            ^~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:5557:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5557:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
                           ^
../tskit/tables.h:630:38: note: expanded from macro 'TSK_REDUCE_TO_SITE_TOPOLOGY'
#define TSK_REDUCE_TO_SITE_TOPOLOGY (1 << 3)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5726:17: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        tables, TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING
                ^
../tskit/tables.h:634:27: note: expanded from macro 'TSK_CHECK_OFFSETS'
#define TSK_CHECK_OFFSETS (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5726:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        tables, TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING
                                    ^
../tskit/tables.h:635:34: note: expanded from macro 'TSK_CHECK_EDGE_ORDERING'
#define TSK_CHECK_EDGE_ORDERING (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5726:63: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        tables, TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING
                                                              ^
../tskit/tables.h:636:34: note: expanded from macro 'TSK_CHECK_SITE_ORDERING'
#define TSK_CHECK_SITE_ORDERING (1 << 2)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5727:23: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
                    | TSK_CHECK_SITE_DUPLICATES);
                      ^
../tskit/tables.h:637:36: note: expanded from macro 'TSK_CHECK_SITE_DUPLICATES'
#define TSK_CHECK_SITE_DUPLICATES (1 << 3)
                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5792:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5792:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
                           ^
../tskit/tables.h:630:38: note: expanded from macro 'TSK_REDUCE_TO_SITE_TOPOLOGY'
#define TSK_REDUCE_TO_SITE_TOPOLOGY (1 << 3)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5866:26: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool keep_unary = !!(self->options & TSK_KEEP_UNARY);
                         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5866:42: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool keep_unary = !!(self->options & TSK_KEEP_UNARY);
                                         ^
../tskit/tables.h:631:25: note: expanded from macro 'TSK_KEEP_UNARY'
#define TSK_KEEP_UNARY (1 << 4)
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6042:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_sites = !!(self->options & TSK_FILTER_SITES);
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6042:44: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_sites = !!(self->options & TSK_FILTER_SITES);
                                           ^
../tskit/tables.h:627:27: note: expanded from macro 'TSK_FILTER_SITES'
#define TSK_FILTER_SITES (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6050:40: warning: redundant cast to the same type [google-readability-casting]
            &self->input_tables.sites, (tsk_id_t) input_site, &site);
                                       ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:6061:17: warning: Value stored to 'mapped_parent' is never read [clang-analyzer-deadcode.DeadStores]
                mapped_parent = TSK_NULL;
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6061:17: note: Value stored to 'mapped_parent' is never read
/home/benj/projects/tskit/c/build/../tskit/tables.c:6063:21: warning: Value stored to 'mapped_parent' is never read [clang-analyzer-deadcode.DeadStores]
                    mapped_parent = self->mutation_id_map[input_parent];
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6063:21: note: Value stored to 'mapped_parent' is never read
/home/benj/projects/tskit/c/build/../tskit/tables.c:6090:25: warning: redundant cast to the same type [google-readability-casting]
                        (tsk_id_t) input_mutation, &mutation);
                        ^~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:6135:34: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_populations = !!(self->options & TSK_FILTER_POPULATIONS);
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6135:50: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_populations = !!(self->options & TSK_FILTER_POPULATIONS);
                                                 ^
../tskit/tables.h:628:33: note: expanded from macro 'TSK_FILTER_POPULATIONS'
#define TSK_FILTER_POPULATIONS (1 << 1)
                                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6144:34: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_individuals = !!(self->options & TSK_FILTER_INDIVIDUALS);
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6144:50: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_individuals = !!(self->options & TSK_FILTER_INDIVIDUALS);
                                                 ^
../tskit/tables.h:629:33: note: expanded from macro 'TSK_FILTER_INDIVIDUALS'
#define TSK_FILTER_INDIVIDUALS (1 << 2)
                                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6230:70: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        &self->input_tables.provenances, &self->tables->provenances, TSK_NO_INIT);
                                                                     ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6380:25: warning: Call to 'calloc' has an allocation size of 0 bytes [clang-analyzer-unix.API]
    bool *parent_seen = calloc(self->nodes.num_rows, sizeof(bool));
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6462:33: note: Assuming the condition is false
    bool check_site_ordering = !!(options & TSK_CHECK_SITE_ORDERING);
                                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6463:35: note: Assuming the condition is false
    bool check_site_duplicates = !!(options & TSK_CHECK_SITE_DUPLICATES);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6464:37: note: Assuming the condition is false
    bool check_mutation_ordering = !!(options & TSK_CHECK_MUTATION_ORDERING);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6466:5: note: Taking false branch
    if (self->sequence_length <= 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6472:17: note: Assuming the condition is false
    for (j = 0; j < self->nodes.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6472:5: note: Loop condition is false. Execution continues on line 6491
    for (j = 0; j < self->nodes.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6491:17: note: Assuming the condition is false
    for (j = 0; j < self->edges.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6491:5: note: Loop condition is false. Execution continues on line 6538
    for (j = 0; j < self->edges.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6538:17: note: Assuming the condition is false
    for (j = 0; j < self->sites.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6538:5: note: Loop condition is false. Execution continues on line 6562
    for (j = 0; j < self->sites.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6562:17: note: Assuming the condition is false
    for (j = 0; j < self->mutations.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6562:5: note: Loop condition is false. Execution continues on line 6602
    for (j = 0; j < self->mutations.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6602:17: note: Assuming the condition is false
    for (j = 0; j < self->migrations.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6602:5: note: Loop condition is false. Execution continues on line 6643
    for (j = 0; j < self->migrations.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6643:10: note: Assuming the condition is true
    if (!!(options & TSK_CHECK_INDEXES)) {
         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6643:5: note: Taking false branch
    if (!!(options & TSK_CHECK_INDEXES)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6663:10: note: Assuming the condition is true
    if (!!(options & TSK_CHECK_OFFSETS)) {
         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6663:5: note: Taking false branch
    if (!!(options & TSK_CHECK_OFFSETS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6669:10: note: Assuming the condition is false
    if (!!(options & TSK_CHECK_EDGE_ORDERING)) {
         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6669:5: note: Taking true branch
    if (!!(options & TSK_CHECK_EDGE_ORDERING)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6670:15: note: Calling 'tsk_table_collection_check_edge_ordering'
        ret = tsk_table_collection_check_edge_ordering(self);
              ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6380:25: note: Call to 'calloc' has an allocation size of 0 bytes
    bool *parent_seen = calloc(self->nodes.num_rows, sizeof(bool));
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6462:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_site_ordering = !!(options & TSK_CHECK_SITE_ORDERING);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6462:45: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_site_ordering = !!(options & TSK_CHECK_SITE_ORDERING);
                                            ^
../tskit/tables.h:636:34: note: expanded from macro 'TSK_CHECK_SITE_ORDERING'
#define TSK_CHECK_SITE_ORDERING (1 << 2)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6463:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_site_duplicates = !!(options & TSK_CHECK_SITE_DUPLICATES);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6463:47: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_site_duplicates = !!(options & TSK_CHECK_SITE_DUPLICATES);
                                              ^
../tskit/tables.h:637:36: note: expanded from macro 'TSK_CHECK_SITE_DUPLICATES'
#define TSK_CHECK_SITE_DUPLICATES (1 << 3)
                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6464:39: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_mutation_ordering = !!(options & TSK_CHECK_MUTATION_ORDERING);
                                      ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6464:49: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_mutation_ordering = !!(options & TSK_CHECK_MUTATION_ORDERING);
                                                ^
../tskit/tables.h:638:38: note: expanded from macro 'TSK_CHECK_MUTATION_ORDERING'
#define TSK_CHECK_MUTATION_ORDERING (1 << 4)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6643:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_INDEXES)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6643:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_INDEXES)) {
                     ^
../tskit/tables.h:639:28: note: expanded from macro 'TSK_CHECK_INDEXES'
#define TSK_CHECK_INDEXES (1 << 5)
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6663:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_OFFSETS)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6663:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_OFFSETS)) {
                     ^
../tskit/tables.h:634:28: note: expanded from macro 'TSK_CHECK_OFFSETS'
#define TSK_CHECK_OFFSETS (1 << 0)
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6669:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_EDGE_ORDERING)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6669:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_EDGE_ORDERING)) {
                     ^
../tskit/tables.h:635:34: note: expanded from macro 'TSK_CHECK_EDGE_ORDERING'
#define TSK_CHECK_EDGE_ORDERING (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6824:54: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_table_collection_check_integrity(self, TSK_CHECK_EDGE_ORDERING);
                                                     ^
../tskit/tables.h:635:34: note: expanded from macro 'TSK_CHECK_EDGE_ORDERING'
#define TSK_CHECK_EDGE_ORDERING (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6879:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6885:59: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_node_table_copy(&self->nodes, &dest->nodes, TSK_NO_INIT);
                                                          ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6889:59: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_edge_table_copy(&self->edges, &dest->edges, TSK_NO_INIT);
                                                          ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6893:74: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_migration_table_copy(&self->migrations, &dest->migrations, TSK_NO_INIT);
                                                                         ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6897:59: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_site_table_copy(&self->sites, &dest->sites, TSK_NO_INIT);
                                                          ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6901:71: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_mutation_table_copy(&self->mutations, &dest->mutations, TSK_NO_INIT);
                                                                      ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6905:77: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_individual_table_copy(&self->individuals, &dest->individuals, TSK_NO_INIT);
                                                                            ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6909:77: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_population_table_copy(&self->populations, &dest->populations, TSK_NO_INIT);
                                                                            ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6913:77: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_provenance_table_copy(&self->provenances, &dest->provenances, TSK_NO_INIT);
                                                                            ^
../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7004:10: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if ((ret ^ (1 << TSK_KAS_ERR_BIT)) == KAS_ERR_KEY_NOT_FOUND) {
         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7004:17: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if ((ret ^ (1 << TSK_KAS_ERR_BIT)) == KAS_ERR_KEY_NOT_FOUND) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7038:24: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            KAS_INT32, TSK_COL_OPTIONAL },
                       ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7040:24: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            KAS_INT32, TSK_COL_OPTIONAL },
                       ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7174:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if ((!(options & TSK_NO_BUILD_INDEXES))
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7174:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if ((!(options & TSK_NO_BUILD_INDEXES))
                     ^
../tskit/tables.h:645:31: note: expanded from macro 'TSK_NO_BUILD_INDEXES'
#define TSK_NO_BUILD_INDEXES (1 << 0)
                              ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7277:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_DEBUG)) {
                     ^
../tskit/tables.h:619:20: note: expanded from macro 'TSK_DEBUG'
#define TSK_DEBUG (1u << 31)
                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:15: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
              ^
../tskit/tables.h:641:6: note: expanded from macro 'TSK_CHECK_ALL'
    (TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING              \
     ^
../tskit/tables.h:634:27: note: expanded from macro 'TSK_CHECK_OFFSETS'
#define TSK_CHECK_OFFSETS (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:31: warning: use of a signed integer operand with a unary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
                              ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:32: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
                               ^
../tskit/tables.h:637:36: note: expanded from macro 'TSK_CHECK_SITE_DUPLICATES'
#define TSK_CHECK_SITE_DUPLICATES (1 << 3)
                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:60: warning: use of a signed integer operand with a unary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
                                                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:61: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
                                                            ^
../tskit/tables.h:639:28: note: expanded from macro 'TSK_CHECK_INDEXES'
#define TSK_CHECK_INDEXES (1 << 5)
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7449:54: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_table_collection_check_integrity(self, TSK_CHECK_ALL);
                                                     ^
../tskit/tables.h:641:6: note: expanded from macro 'TSK_CHECK_ALL'
    (TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING              \
     ^
../tskit/tables.h:634:27: note: expanded from macro 'TSK_CHECK_OFFSETS'
#define TSK_CHECK_OFFSETS (1 << 0)
                          ^
../tskit/tables.h:673:5: warning: function 'tsk_individual_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_individual_table_init(tsk_individual_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:322:1: note: the definition seen here
tsk_individual_table_init(tsk_individual_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
../tskit/tables.h:673:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_individual_table_init(tsk_individual_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:816:5: warning: function 'tsk_individual_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_individual_table_set_columns(tsk_individual_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:378:1: note: the definition seen here
tsk_individual_table_set_columns(tsk_individual_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:816:5: note: differing parameters are named here: ('location_length', 'metadata_length'), in definition: ('location_offset', 'metadata_offset')
int tsk_individual_table_set_columns(tsk_individual_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:819:5: warning: function 'tsk_individual_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_individual_table_append_columns(tsk_individual_table_t *self,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:395:1: note: the definition seen here
tsk_individual_table_append_columns(tsk_individual_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:819:5: note: differing parameters are named here: ('location_length', 'metadata_length'), in definition: ('location_offset', 'metadata_offset')
int tsk_individual_table_append_columns(tsk_individual_table_t *self,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:849:5: warning: function 'tsk_node_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_node_table_init(tsk_node_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:867:1: note: the definition seen here
tsk_node_table_init(tsk_node_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:849:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_node_table_init(tsk_node_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:987:5: warning: function 'tsk_node_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_node_table_set_columns(tsk_node_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:915:1: note: the definition seen here
tsk_node_table_set_columns(tsk_node_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:987:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_node_table_set_columns(tsk_node_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:990:5: warning: function 'tsk_node_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_node_table_append_columns(tsk_node_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:932:1: note: the definition seen here
tsk_node_table_append_columns(tsk_node_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:990:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_node_table_append_columns(tsk_node_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1014:5: warning: function 'tsk_edge_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_edge_table_init(tsk_edge_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1353:1: note: the definition seen here
tsk_edge_table_init(tsk_edge_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1014:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_edge_table_init(tsk_edge_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1151:5: warning: function 'tsk_edge_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_edge_table_set_columns(tsk_edge_table_t *self, tsk_size_t num_rows, double *left,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1433:1: note: the definition seen here
tsk_edge_table_set_columns(tsk_edge_table_t *self, tsk_size_t num_rows, double *left,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1151:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_edge_table_set_columns(tsk_edge_table_t *self, tsk_size_t num_rows, double *left,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1154:5: warning: function 'tsk_edge_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_edge_table_append_columns(tsk_edge_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1450:1: note: the definition seen here
tsk_edge_table_append_columns(tsk_edge_table_t *self, tsk_size_t num_rows, double *left,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1154:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_edge_table_append_columns(tsk_edge_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1180:5: warning: function 'tsk_migration_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2971:1: note: the definition seen here
tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1180:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1319:5: warning: function 'tsk_migration_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2971:1: note: the definition seen here
tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1319:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1324:5: warning: function 'tsk_migration_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_migration_table_set_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3079:1: note: the definition seen here
tsk_migration_table_set_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1324:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_migration_table_set_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1327:5: warning: function 'tsk_migration_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_migration_table_append_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2998:1: note: the definition seen here
tsk_migration_table_append_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1327:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_migration_table_append_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1351:5: warning: function 'tsk_site_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_site_table_init(tsk_site_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1880:1: note: the definition seen here
tsk_site_table_init(tsk_site_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1351:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_site_table_init(tsk_site_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1490:5: warning: function 'tsk_site_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_site_table_set_columns(tsk_site_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2051:1: note: the definition seen here
tsk_site_table_set_columns(tsk_site_table_t *self, tsk_size_t num_rows, double *position,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1490:5: note: differing parameters are named here: ('ancestral_state_length', 'metadata_length'), in definition: ('ancestral_state_offset', 'metadata_offset')
int tsk_site_table_set_columns(tsk_site_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1493:5: warning: function 'tsk_site_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_site_table_append_columns(tsk_site_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1955:1: note: the definition seen here
tsk_site_table_append_columns(tsk_site_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1493:5: note: differing parameters are named here: ('ancestral_state_length', 'metadata_length'), in definition: ('ancestral_state_offset', 'metadata_offset')
int tsk_site_table_append_columns(tsk_site_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1517:5: warning: function 'tsk_mutation_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_init(tsk_mutation_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2428:1: note: the definition seen here
tsk_mutation_table_init(tsk_mutation_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1517:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_mutation_table_init(tsk_mutation_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1574:5: warning: function 'tsk_mutation_table_truncate' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_truncate(tsk_mutation_table_t *self, tsk_size_t num_rows);
    ^                                                 ~~~~~
                                                      mutations
/home/benj/projects/tskit/c/build/../tskit/tables.c:2666:1: note: the definition seen here
tsk_mutation_table_truncate(tsk_mutation_table_t *mutations, tsk_size_t num_rows)
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1574:5: note: differing parameters are named here: ('self'), in definition: ('mutations')
int tsk_mutation_table_truncate(tsk_mutation_table_t *self, tsk_size_t num_rows);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1659:5: warning: function 'tsk_mutation_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_set_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2609:1: note: the definition seen here
tsk_mutation_table_set_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1659:5: note: differing parameters are named here: ('derived_state_length', 'metadata_length'), in definition: ('derived_state_offset', 'metadata_offset')
int tsk_mutation_table_set_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1662:5: warning: function 'tsk_mutation_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_append_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2505:1: note: the definition seen here
tsk_mutation_table_append_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1662:5: note: differing parameters are named here: ('derived_state_length', 'metadata_length'), in definition: ('derived_state_offset', 'metadata_offset')
int tsk_mutation_table_append_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1667:5: warning: function 'tsk_mutation_table_truncate' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_truncate(tsk_mutation_table_t *self, tsk_size_t num_rows);
    ^                                                 ~~~~~
                                                      mutations
/home/benj/projects/tskit/c/build/../tskit/tables.c:2666:1: note: the definition seen here
tsk_mutation_table_truncate(tsk_mutation_table_t *mutations, tsk_size_t num_rows)
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1667:5: note: differing parameters are named here: ('self'), in definition: ('mutations')
int tsk_mutation_table_truncate(tsk_mutation_table_t *self, tsk_size_t num_rows);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1695:5: warning: function 'tsk_population_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_population_table_init(tsk_population_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3434:1: note: the definition seen here
tsk_population_table_init(tsk_population_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1695:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_population_table_init(tsk_population_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1854:5: warning: function 'tsk_provenance_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_provenance_table_init(tsk_provenance_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3882:1: note: the definition seen here
tsk_provenance_table_init(tsk_provenance_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1854:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_provenance_table_init(tsk_provenance_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2018:5: warning: function 'tsk_table_collection_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_init(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6695:1: note: the definition seen here
tsk_table_collection_init(tsk_table_collection_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2018:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_init(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2189:5: warning: function 'tsk_table_collection_record_num_rows' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_record_num_rows(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7541:1: note: the definition seen here
tsk_table_collection_record_num_rows(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2189:5: note: differing parameters are named here: ('bookmark'), in definition: ('position')
int tsk_table_collection_record_num_rows(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2206:5: warning: function 'tsk_table_collection_truncate' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_truncate(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7556:1: note: the definition seen here
tsk_table_collection_truncate(tsk_table_collection_t *tables, tsk_bookmark_t *position)
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2206:5: note: differing parameters are named here: ('self', 'bookmark'), in definition: ('tables', 'position')
int tsk_table_collection_truncate(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2327:6: warning: function 'tsk_table_collection_has_index' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
bool tsk_table_collection_has_index(tsk_table_collection_t *self, tsk_flags_t options);
     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6794:1: note: the definition seen here
tsk_table_collection_has_index(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2327:6: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
bool tsk_table_collection_has_index(tsk_table_collection_t *self, tsk_flags_t options);
     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2342:5: warning: function 'tsk_table_collection_drop_index' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_drop_index(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6802:1: note: the definition seen here
tsk_table_collection_drop_index(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2342:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_drop_index(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2357:5: warning: function 'tsk_table_collection_build_index' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_build_index(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6813:1: note: the definition seen here
tsk_table_collection_build_index(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2357:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_build_index(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2362:5: warning: function 'tsk_table_collection_link_ancestors' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_link_ancestors(tsk_table_collection_t *self, tsk_id_t *samples,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7289:1: note: the definition seen here
tsk_table_collection_link_ancestors(tsk_table_collection_t *self, tsk_id_t *samples,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2362:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_link_ancestors(tsk_table_collection_t *self, tsk_id_t *samples,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2366:5: warning: function 'tsk_table_collection_deduplicate_sites' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_deduplicate_sites(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7354:1: note: the definition seen here
tsk_table_collection_deduplicate_sites(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2366:5: note: differing parameters are named here: ('tables', 'options'), in definition: ('self', 'TSK_UNUSED_options')
int tsk_table_collection_deduplicate_sites(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2368:5: warning: function 'tsk_table_collection_compute_mutation_parents' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_compute_mutation_parents(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7426:1: note: the definition seen here
tsk_table_collection_compute_mutation_parents(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2368:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_compute_mutation_parents(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/tables.c:117:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        } else if (!(read_cols[j].options & TSK_COL_OPTIONAL)) {
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:117:45: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        } else if (!(read_cols[j].options & TSK_COL_OPTIONAL)) {
                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:146:44: warning: pointer parameter 'offsets' can be pointer to const [readability-non-const-parameter]
check_offsets(size_t num_rows, tsk_size_t *offsets, tsk_size_t length, bool check_length)
                               ~~~~~~~~~~  ^
                               const 
/home/benj/projects/tskit/c/build/../tskit/tables.c:295:32: warning: redundant cast to the same type [google-readability-casting]
    self->max_rows_increment = (tsk_size_t) max_rows_increment;
                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:306:43: warning: redundant cast to the same type [google-readability-casting]
    self->max_metadata_length_increment = (tsk_size_t) max_metadata_length_increment;
                                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:317:43: warning: redundant cast to the same type [google-readability-casting]
    self->max_location_length_increment = (tsk_size_t) max_location_length_increment;
                                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:360:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:414:58: warning: redundant cast to the same type [google-readability-casting]
    ret = tsk_individual_table_expand_main_columns(self, (tsk_size_t) num_rows);
                                                         ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:422:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->location_length;
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:431:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->location_length + location_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:445:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length;
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:454:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length + metadata_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:465:23: warning: redundant cast to the same type [google-readability-casting]
    self->num_rows += (tsk_size_t) num_rows;
                      ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:504:54: warning: redundant cast to the same type [google-readability-casting]
    ret = tsk_individual_table_expand_location(self, (tsk_size_t) location_length);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:508:54: warning: redundant cast to the same type [google-readability-casting]
    ret = tsk_individual_table_expand_metadata(self, (tsk_size_t) metadata_length);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:513:9: warning: redundant cast to the same type [google-readability-casting]
        (tsk_size_t) location_length, metadata, (tsk_size_t) metadata_length);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:513:49: warning: redundant cast to the same type [google-readability-casting]
        (tsk_size_t) location_length, metadata, (tsk_size_t) metadata_length);
                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:600:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:747:52: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            &metadata_schema_length, 0, KAS_UINT8, TSK_COL_OPTIONAL },
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:897:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:964:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length + metadata_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:989:23: warning: redundant cast to the same type [google-readability-casting]
    self->num_rows += (tsk_size_t) num_rows;
                      ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1184:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1236:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            0, KAS_UINT8, TSK_COL_OPTIONAL },
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1396:5: warning: Null pointer passed as an argument to a 'nonnull' parameter [clang-analyzer-core.NonNullParamChecker]
    memcpy(self->metadata + self->metadata_length, metadata, metadata_length);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5974:5: note: Loop condition is false. Execution continues on line 5991
    for (j = start; j < end; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5991:11: note: Calling 'simplifier_merge_ancestors'
    ret = simplifier_merge_ancestors(self, parent);
          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5865:22: note: Assuming the condition is false
    bool is_sample = output_id != TSK_NULL;
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5866:24: note: Assuming the condition is false
    bool keep_unary = !!(self->options & TSK_KEEP_UNARY);
                       ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5868:5: note: Taking false branch
    if (is_sample) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5878:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5882:12: note: Assuming the condition is true
    while ((ret = segment_overlapper_next(
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5882:5: note: Loop condition is true.  Entering loop body
    while ((ret = segment_overlapper_next(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5887:13: note: Assuming 'num_overlapping' is not equal to 1
        if (num_overlapping == 1) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5887:9: note: Taking false branch
        if (num_overlapping == 1) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5905:13: note: Taking true branch
            if (output_id == TSK_NULL) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5907:17: note: Taking false branch
                if (ret < 0) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5913:13: note: Loop condition is true.  Entering loop body
            for (j = 0; j < num_overlapping; j++) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5915:17: note: Taking false branch
                if (ret != 0) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5913:13: note: Loop condition is true.  Entering loop body
            for (j = 0; j < num_overlapping; j++) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5915:17: note: Taking false branch
                if (ret != 0) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5913:25: note: Assuming 'j' is >= 'num_overlapping'
            for (j = 0; j < num_overlapping; j++) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5913:13: note: Loop condition is false. Execution continues on line 5920
            for (j = 0; j < num_overlapping; j++) {
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5920:23: note: Left side of '&&' is false
        if (is_sample && left != prev_right) {
                      ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5927:9: note: Taking true branch
        if (keep_unary) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5931:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5882:12: note: Assuming the condition is false
    while ((ret = segment_overlapper_next(
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5882:5: note: Loop condition is false. Execution continues on line 5937
    while ((ret = segment_overlapper_next(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5937:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5937:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5940:19: note: Left side of '&&' is false
    if (is_sample && prev_right != self->tables->sequence_length) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5948:9: note: Assuming the condition is true
    if (output_id != TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5948:5: note: Taking true branch
    if (output_id != TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5949:15: note: Calling 'simplifier_flush_edges'
        ret = simplifier_flush_edges(self, output_id, &num_flushed_edges);
              ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5479:17: note: Assuming the condition is true
    for (j = 0; j < self->num_buffered_children; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5479:5: note: Loop condition is true.  Entering loop body
    for (j = 0; j < self->num_buffered_children; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5481:52: note: Assuming 'x' is equal to NULL
        for (x = self->child_edge_map_head[child]; x != NULL; x = x->next) {
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5481:9: note: Loop condition is false. Execution continues on line 5489
        for (x = self->child_edge_map_head[child]; x != NULL; x = x->next) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5479:17: note: Assuming the condition is true
    for (j = 0; j < self->num_buffered_children; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5479:5: note: Loop condition is true.  Entering loop body
    for (j = 0; j < self->num_buffered_children; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5481:52: note: Assuming 'x' is not equal to NULL
        for (x = self->child_edge_map_head[child]; x != NULL; x = x->next) {
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5481:9: note: Loop condition is true.  Entering loop body
        for (x = self->child_edge_map_head[child]; x != NULL; x = x->next) {
        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5483:73: note: Passing null pointer value via 6th parameter 'metadata'
                &self->tables->edges, x->left, x->right, parent, child, NULL, 0);
                                                                        ^
/usr/lib/llvm-6.0/bin/../lib/clang/6.0.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5482:19: note: Calling 'tsk_edge_table_add_row'
            ret = tsk_edge_table_add_row(
                  ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1386:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1390:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1396:5: note: Null pointer passed as an argument to a 'nonnull' parameter
    memcpy(self->metadata + self->metadata_length, metadata, metadata_length);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1415:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1485:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length + metadata_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1634:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1683:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            TSK_COL_OPTIONAL },
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1685:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            TSK_COL_OPTIONAL },
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1687:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            0, KAS_UINT8, TSK_COL_OPTIONAL },
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1927:30: warning: redundant cast to the same type [google-readability-casting]
    ancestral_state_offset = (tsk_size_t) self->ancestral_state_length;
                             ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:1938:23: warning: redundant cast to the same type [google-readability-casting]
    metadata_offset = (tsk_size_t) self->metadata_length;
                      ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:2032:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2164:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:2269:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            0, KAS_UINT8, TSK_COL_OPTIONAL },
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2365:42: warning: redundant cast to the same type [google-readability-casting]
        self->max_derived_state_length = (tsk_size_t) new_size;
                                         ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:2590:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2729:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:2839:52: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            &metadata_schema_length, 0, KAS_UINT8, TSK_COL_OPTIONAL },
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3036:19: warning: redundant cast to the same type [google-readability-casting]
                = (tsk_size_t) self->metadata_length + metadata_offset[j];
                  ^~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:3060:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3192:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:3324:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            TSK_COL_OPTIONAL },
            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3326:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            KAS_UINT32, TSK_COL_OPTIONAL },
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3328:52: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            &metadata_schema_length, 0, KAS_UINT8, TSK_COL_OPTIONAL },
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3465:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3639:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:3742:52: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            &metadata_schema_length, 0, KAS_UINT8, TSK_COL_OPTIONAL },
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3919:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:4127:15: warning: redundant cast to the same type [google-readability-casting]
    row->id = (tsk_id_t) index;
              ^~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:4329:56: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_table_collection_check_integrity(tables, TSK_CHECK_OFFSETS);
                                                       ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:634:28: note: expanded from macro 'TSK_CHECK_OFFSETS'
#define TSK_CHECK_OFFSETS (1 << 0)
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:4940:67: warning: pointer parameter 'ancestors' can be pointer to const [readability-non-const-parameter]
ancestor_mapper_init_ancestors(ancestor_mapper_t *self, tsk_id_t *ancestors)
                                                        ~~~~~~~~  ^
                                                        const 
/home/benj/projects/tskit/c/build/../tskit/tables.c:5336:54: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        out, "\tfilter_unreferenced_sites: %d\n", !!(self->options & TSK_FILTER_SITES));
                                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5336:70: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        out, "\tfilter_unreferenced_sites: %d\n", !!(self->options & TSK_FILTER_SITES));
                                                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:627:27: note: expanded from macro 'TSK_FILTER_SITES'
#define TSK_FILTER_SITES (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5338:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        !!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY));
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5338:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        !!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY));
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:630:38: note: expanded from macro 'TSK_REDUCE_TO_SITE_TOPOLOGY'
#define TSK_REDUCE_TO_SITE_TOPOLOGY (1 << 3)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5339:45: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    fprintf(out, "\tkeep_unary  : %d\n", !!(self->options & TSK_KEEP_UNARY));
                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5339:61: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    fprintf(out, "\tkeep_unary  : %d\n", !!(self->options & TSK_KEEP_UNARY));
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:631:25: note: expanded from macro 'TSK_KEEP_UNARY'
#define TSK_KEEP_UNARY (1 << 4)
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5393:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5393:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:630:38: note: expanded from macro 'TSK_REDUCE_TO_SITE_TOPOLOGY'
#define TSK_REDUCE_TO_SITE_TOPOLOGY (1 << 3)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5444:61: warning: redundant cast to the same type [google-readability-casting]
    ret = tsk_node_table_get_row(&self->input_tables.nodes, (tsk_id_t) input_id, &node);
                                                            ^~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:5557:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5557:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:630:38: note: expanded from macro 'TSK_REDUCE_TO_SITE_TOPOLOGY'
#define TSK_REDUCE_TO_SITE_TOPOLOGY (1 << 3)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5726:17: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        tables, TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:634:27: note: expanded from macro 'TSK_CHECK_OFFSETS'
#define TSK_CHECK_OFFSETS (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5726:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        tables, TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING
                                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:635:34: note: expanded from macro 'TSK_CHECK_EDGE_ORDERING'
#define TSK_CHECK_EDGE_ORDERING (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5726:63: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        tables, TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING
                                                              ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:636:34: note: expanded from macro 'TSK_CHECK_SITE_ORDERING'
#define TSK_CHECK_SITE_ORDERING (1 << 2)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5727:23: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
                    | TSK_CHECK_SITE_DUPLICATES);
                      ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:637:36: note: expanded from macro 'TSK_CHECK_SITE_DUPLICATES'
#define TSK_CHECK_SITE_DUPLICATES (1 << 3)
                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5792:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5792:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(self->options & TSK_REDUCE_TO_SITE_TOPOLOGY)) {
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:630:38: note: expanded from macro 'TSK_REDUCE_TO_SITE_TOPOLOGY'
#define TSK_REDUCE_TO_SITE_TOPOLOGY (1 << 3)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5866:26: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool keep_unary = !!(self->options & TSK_KEEP_UNARY);
                         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:5866:42: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool keep_unary = !!(self->options & TSK_KEEP_UNARY);
                                         ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:631:25: note: expanded from macro 'TSK_KEEP_UNARY'
#define TSK_KEEP_UNARY (1 << 4)
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6042:28: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_sites = !!(self->options & TSK_FILTER_SITES);
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6042:44: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_sites = !!(self->options & TSK_FILTER_SITES);
                                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:627:27: note: expanded from macro 'TSK_FILTER_SITES'
#define TSK_FILTER_SITES (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6050:40: warning: redundant cast to the same type [google-readability-casting]
            &self->input_tables.sites, (tsk_id_t) input_site, &site);
                                       ^~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:6061:17: warning: Value stored to 'mapped_parent' is never read [clang-analyzer-deadcode.DeadStores]
                mapped_parent = TSK_NULL;
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6061:17: note: Value stored to 'mapped_parent' is never read
/home/benj/projects/tskit/c/build/../tskit/tables.c:6063:21: warning: Value stored to 'mapped_parent' is never read [clang-analyzer-deadcode.DeadStores]
                    mapped_parent = self->mutation_id_map[input_parent];
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6063:21: note: Value stored to 'mapped_parent' is never read
/home/benj/projects/tskit/c/build/../tskit/tables.c:6090:25: warning: redundant cast to the same type [google-readability-casting]
                        (tsk_id_t) input_mutation, &mutation);
                        ^~~~~~~~~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/tables.c:6135:34: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_populations = !!(self->options & TSK_FILTER_POPULATIONS);
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6135:50: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_populations = !!(self->options & TSK_FILTER_POPULATIONS);
                                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:628:33: note: expanded from macro 'TSK_FILTER_POPULATIONS'
#define TSK_FILTER_POPULATIONS (1 << 1)
                                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6144:34: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_individuals = !!(self->options & TSK_FILTER_INDIVIDUALS);
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6144:50: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool filter_individuals = !!(self->options & TSK_FILTER_INDIVIDUALS);
                                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:629:33: note: expanded from macro 'TSK_FILTER_INDIVIDUALS'
#define TSK_FILTER_INDIVIDUALS (1 << 2)
                                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6230:70: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        &self->input_tables.provenances, &self->tables->provenances, TSK_NO_INIT);
                                                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6380:25: warning: Call to 'calloc' has an allocation size of 0 bytes [clang-analyzer-unix.API]
    bool *parent_seen = calloc(self->nodes.num_rows, sizeof(bool));
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6462:33: note: Assuming the condition is false
    bool check_site_ordering = !!(options & TSK_CHECK_SITE_ORDERING);
                                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6463:35: note: Assuming the condition is false
    bool check_site_duplicates = !!(options & TSK_CHECK_SITE_DUPLICATES);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6464:37: note: Assuming the condition is false
    bool check_mutation_ordering = !!(options & TSK_CHECK_MUTATION_ORDERING);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6466:5: note: Taking false branch
    if (self->sequence_length <= 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6472:17: note: Assuming the condition is false
    for (j = 0; j < self->nodes.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6472:5: note: Loop condition is false. Execution continues on line 6491
    for (j = 0; j < self->nodes.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6491:17: note: Assuming the condition is false
    for (j = 0; j < self->edges.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6491:5: note: Loop condition is false. Execution continues on line 6538
    for (j = 0; j < self->edges.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6538:17: note: Assuming the condition is false
    for (j = 0; j < self->sites.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6538:5: note: Loop condition is false. Execution continues on line 6562
    for (j = 0; j < self->sites.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6562:17: note: Assuming the condition is false
    for (j = 0; j < self->mutations.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6562:5: note: Loop condition is false. Execution continues on line 6602
    for (j = 0; j < self->mutations.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6602:17: note: Assuming the condition is false
    for (j = 0; j < self->migrations.num_rows; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6602:5: note: Loop condition is false. Execution continues on line 6643
    for (j = 0; j < self->migrations.num_rows; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6643:10: note: Assuming the condition is true
    if (!!(options & TSK_CHECK_INDEXES)) {
         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6643:5: note: Taking false branch
    if (!!(options & TSK_CHECK_INDEXES)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6663:10: note: Assuming the condition is true
    if (!!(options & TSK_CHECK_OFFSETS)) {
         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6663:5: note: Taking false branch
    if (!!(options & TSK_CHECK_OFFSETS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6669:10: note: Assuming the condition is false
    if (!!(options & TSK_CHECK_EDGE_ORDERING)) {
         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6669:5: note: Taking true branch
    if (!!(options & TSK_CHECK_EDGE_ORDERING)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6670:15: note: Calling 'tsk_table_collection_check_edge_ordering'
        ret = tsk_table_collection_check_edge_ordering(self);
              ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6380:25: note: Call to 'calloc' has an allocation size of 0 bytes
    bool *parent_seen = calloc(self->nodes.num_rows, sizeof(bool));
                        ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6462:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_site_ordering = !!(options & TSK_CHECK_SITE_ORDERING);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6462:45: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_site_ordering = !!(options & TSK_CHECK_SITE_ORDERING);
                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:636:34: note: expanded from macro 'TSK_CHECK_SITE_ORDERING'
#define TSK_CHECK_SITE_ORDERING (1 << 2)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6463:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_site_duplicates = !!(options & TSK_CHECK_SITE_DUPLICATES);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6463:47: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_site_duplicates = !!(options & TSK_CHECK_SITE_DUPLICATES);
                                              ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:637:36: note: expanded from macro 'TSK_CHECK_SITE_DUPLICATES'
#define TSK_CHECK_SITE_DUPLICATES (1 << 3)
                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6464:39: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_mutation_ordering = !!(options & TSK_CHECK_MUTATION_ORDERING);
                                      ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6464:49: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool check_mutation_ordering = !!(options & TSK_CHECK_MUTATION_ORDERING);
                                                ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:638:38: note: expanded from macro 'TSK_CHECK_MUTATION_ORDERING'
#define TSK_CHECK_MUTATION_ORDERING (1 << 4)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6474:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [clang-diagnostic-conversion]
        if (!isfinite(node_time)) {
                      ^
/usr/include/math.h:629:50: note: expanded from macro 'isfinite'
#  define isfinite(x) __MATH_TG ((x), __finite, (x))
                                                 ^
/usr/include/math.h:559:16: note: expanded from macro '__MATH_TG'
   ? FUNC ## f ARGS                             \
               ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6514:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [clang-diagnostic-conversion]
        if (!(isfinite(left) && isfinite(right))) {
                       ^
/usr/include/math.h:629:50: note: expanded from macro 'isfinite'
#  define isfinite(x) __MATH_TG ((x), __finite, (x))
                                                 ^
/usr/include/math.h:559:16: note: expanded from macro '__MATH_TG'
   ? FUNC ## f ARGS                             \
               ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6514:42: warning: implicit conversion loses floating-point precision: 'double' to 'float' [clang-diagnostic-conversion]
        if (!(isfinite(left) && isfinite(right))) {
                                         ^
/usr/include/math.h:629:50: note: expanded from macro 'isfinite'
#  define isfinite(x) __MATH_TG ((x), __finite, (x))
                                                 ^
/usr/include/math.h:559:16: note: expanded from macro '__MATH_TG'
   ? FUNC ## f ARGS                             \
               ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6541:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [clang-diagnostic-conversion]
        if (!isfinite(position)) {
                      ^
/usr/include/math.h:629:50: note: expanded from macro 'isfinite'
#  define isfinite(x) __MATH_TG ((x), __finite, (x))
                                                 ^
/usr/include/math.h:559:16: note: expanded from macro '__MATH_TG'
   ? FUNC ## f ARGS                             \
               ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6617:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [clang-diagnostic-conversion]
        if (!isfinite(self->migrations.time[j])) {
                      ^
/usr/include/math.h:629:50: note: expanded from macro 'isfinite'
#  define isfinite(x) __MATH_TG ((x), __finite, (x))
                                                 ^
/usr/include/math.h:559:16: note: expanded from macro '__MATH_TG'
   ? FUNC ## f ARGS                             \
               ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6625:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [clang-diagnostic-conversion]
        if (!(isfinite(left) && isfinite(right))) {
                       ^
/usr/include/math.h:629:50: note: expanded from macro 'isfinite'
#  define isfinite(x) __MATH_TG ((x), __finite, (x))
                                                 ^
/usr/include/math.h:559:16: note: expanded from macro '__MATH_TG'
   ? FUNC ## f ARGS                             \
               ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6625:42: warning: implicit conversion loses floating-point precision: 'double' to 'float' [clang-diagnostic-conversion]
        if (!(isfinite(left) && isfinite(right))) {
                                         ^
/usr/include/math.h:629:50: note: expanded from macro 'isfinite'
#  define isfinite(x) __MATH_TG ((x), __finite, (x))
                                                 ^
/usr/include/math.h:559:16: note: expanded from macro '__MATH_TG'
   ? FUNC ## f ARGS                             \
               ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6643:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_INDEXES)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6643:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_INDEXES)) {
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:639:28: note: expanded from macro 'TSK_CHECK_INDEXES'
#define TSK_CHECK_INDEXES (1 << 5)
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6663:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_OFFSETS)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6663:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_OFFSETS)) {
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:634:28: note: expanded from macro 'TSK_CHECK_OFFSETS'
#define TSK_CHECK_OFFSETS (1 << 0)
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6669:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_EDGE_ORDERING)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6669:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_CHECK_EDGE_ORDERING)) {
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:635:34: note: expanded from macro 'TSK_CHECK_EDGE_ORDERING'
#define TSK_CHECK_EDGE_ORDERING (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6824:54: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_table_collection_check_integrity(self, TSK_CHECK_EDGE_ORDERING);
                                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:635:34: note: expanded from macro 'TSK_CHECK_EDGE_ORDERING'
#define TSK_CHECK_EDGE_ORDERING (1 << 1)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6879:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6885:59: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_node_table_copy(&self->nodes, &dest->nodes, TSK_NO_INIT);
                                                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6889:59: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_edge_table_copy(&self->edges, &dest->edges, TSK_NO_INIT);
                                                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6893:74: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_migration_table_copy(&self->migrations, &dest->migrations, TSK_NO_INIT);
                                                                         ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6897:59: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_site_table_copy(&self->sites, &dest->sites, TSK_NO_INIT);
                                                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6901:71: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_mutation_table_copy(&self->mutations, &dest->mutations, TSK_NO_INIT);
                                                                      ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6905:77: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_individual_table_copy(&self->individuals, &dest->individuals, TSK_NO_INIT);
                                                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6909:77: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_population_table_copy(&self->populations, &dest->populations, TSK_NO_INIT);
                                                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6913:77: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_provenance_table_copy(&self->provenances, &dest->provenances, TSK_NO_INIT);
                                                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7004:10: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if ((ret ^ (1 << TSK_KAS_ERR_BIT)) == KAS_ERR_KEY_NOT_FOUND) {
         ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7004:17: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if ((ret ^ (1 << TSK_KAS_ERR_BIT)) == KAS_ERR_KEY_NOT_FOUND) {
                ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7038:24: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            KAS_INT32, TSK_COL_OPTIONAL },
                       ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7040:24: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
            KAS_INT32, TSK_COL_OPTIONAL },
                       ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:40:27: note: expanded from macro 'TSK_COL_OPTIONAL'
#define TSK_COL_OPTIONAL (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7174:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if ((!(options & TSK_NO_BUILD_INDEXES))
           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7174:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if ((!(options & TSK_NO_BUILD_INDEXES))
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:645:31: note: expanded from macro 'TSK_NO_BUILD_INDEXES'
#define TSK_NO_BUILD_INDEXES (1 << 0)
                              ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7277:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_DEBUG)) {
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:619:20: note: expanded from macro 'TSK_DEBUG'
#define TSK_DEBUG (1u << 31)
                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:15: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
              ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:641:6: note: expanded from macro 'TSK_CHECK_ALL'
    (TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING              \
     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:634:27: note: expanded from macro 'TSK_CHECK_OFFSETS'
#define TSK_CHECK_OFFSETS (1 << 0)
                          ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:31: warning: use of a signed integer operand with a unary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
                              ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:32: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
                               ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:637:36: note: expanded from macro 'TSK_CHECK_SITE_DUPLICATES'
#define TSK_CHECK_SITE_DUPLICATES (1 << 3)
                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:60: warning: use of a signed integer operand with a unary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
                                                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7378:61: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        self, TSK_CHECK_ALL & ~TSK_CHECK_SITE_DUPLICATES & ~TSK_CHECK_INDEXES);
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:639:28: note: expanded from macro 'TSK_CHECK_INDEXES'
#define TSK_CHECK_INDEXES (1 << 5)
                           ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7449:54: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_table_collection_check_integrity(self, TSK_CHECK_ALL);
                                                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:641:52: note: expanded from macro 'TSK_CHECK_ALL'
    (TSK_CHECK_OFFSETS | TSK_CHECK_EDGE_ORDERING | TSK_CHECK_SITE_ORDERING              \
                                                   ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:636:34: note: expanded from macro 'TSK_CHECK_SITE_ORDERING'
#define TSK_CHECK_SITE_ORDERING (1 << 2)
                                 ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:673:5: warning: function 'tsk_individual_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_individual_table_init(tsk_individual_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:322:1: note: the definition seen here
tsk_individual_table_init(tsk_individual_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:673:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_individual_table_init(tsk_individual_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:816:5: warning: function 'tsk_individual_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_individual_table_set_columns(tsk_individual_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:378:1: note: the definition seen here
tsk_individual_table_set_columns(tsk_individual_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:816:5: note: differing parameters are named here: ('location_length', 'metadata_length'), in definition: ('location_offset', 'metadata_offset')
int tsk_individual_table_set_columns(tsk_individual_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:819:5: warning: function 'tsk_individual_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_individual_table_append_columns(tsk_individual_table_t *self,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:395:1: note: the definition seen here
tsk_individual_table_append_columns(tsk_individual_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:819:5: note: differing parameters are named here: ('location_length', 'metadata_length'), in definition: ('location_offset', 'metadata_offset')
int tsk_individual_table_append_columns(tsk_individual_table_t *self,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:849:5: warning: function 'tsk_node_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_node_table_init(tsk_node_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:867:1: note: the definition seen here
tsk_node_table_init(tsk_node_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:849:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_node_table_init(tsk_node_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:987:5: warning: function 'tsk_node_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_node_table_set_columns(tsk_node_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:915:1: note: the definition seen here
tsk_node_table_set_columns(tsk_node_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:987:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_node_table_set_columns(tsk_node_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:990:5: warning: function 'tsk_node_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_node_table_append_columns(tsk_node_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:932:1: note: the definition seen here
tsk_node_table_append_columns(tsk_node_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:990:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_node_table_append_columns(tsk_node_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1014:5: warning: function 'tsk_edge_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_edge_table_init(tsk_edge_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1353:1: note: the definition seen here
tsk_edge_table_init(tsk_edge_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1014:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_edge_table_init(tsk_edge_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1151:5: warning: function 'tsk_edge_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_edge_table_set_columns(tsk_edge_table_t *self, tsk_size_t num_rows, double *left,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1433:1: note: the definition seen here
tsk_edge_table_set_columns(tsk_edge_table_t *self, tsk_size_t num_rows, double *left,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1151:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_edge_table_set_columns(tsk_edge_table_t *self, tsk_size_t num_rows, double *left,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1154:5: warning: function 'tsk_edge_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_edge_table_append_columns(tsk_edge_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1450:1: note: the definition seen here
tsk_edge_table_append_columns(tsk_edge_table_t *self, tsk_size_t num_rows, double *left,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1154:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_edge_table_append_columns(tsk_edge_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1180:5: warning: function 'tsk_migration_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2971:1: note: the definition seen here
tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1180:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1319:5: warning: function 'tsk_migration_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2971:1: note: the definition seen here
tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1319:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_migration_table_init(tsk_migration_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1324:5: warning: function 'tsk_migration_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_migration_table_set_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3079:1: note: the definition seen here
tsk_migration_table_set_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1324:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_migration_table_set_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1327:5: warning: function 'tsk_migration_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_migration_table_append_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2998:1: note: the definition seen here
tsk_migration_table_append_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1327:5: note: differing parameters are named here: ('metadata_length'), in definition: ('metadata_offset')
int tsk_migration_table_append_columns(tsk_migration_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1351:5: warning: function 'tsk_site_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_site_table_init(tsk_site_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1880:1: note: the definition seen here
tsk_site_table_init(tsk_site_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1351:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_site_table_init(tsk_site_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1490:5: warning: function 'tsk_site_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_site_table_set_columns(tsk_site_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2051:1: note: the definition seen here
tsk_site_table_set_columns(tsk_site_table_t *self, tsk_size_t num_rows, double *position,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1490:5: note: differing parameters are named here: ('ancestral_state_length', 'metadata_length'), in definition: ('ancestral_state_offset', 'metadata_offset')
int tsk_site_table_set_columns(tsk_site_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1493:5: warning: function 'tsk_site_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_site_table_append_columns(tsk_site_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:1955:1: note: the definition seen here
tsk_site_table_append_columns(tsk_site_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1493:5: note: differing parameters are named here: ('ancestral_state_length', 'metadata_length'), in definition: ('ancestral_state_offset', 'metadata_offset')
int tsk_site_table_append_columns(tsk_site_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1517:5: warning: function 'tsk_mutation_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_init(tsk_mutation_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2428:1: note: the definition seen here
tsk_mutation_table_init(tsk_mutation_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1517:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_mutation_table_init(tsk_mutation_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1574:5: warning: function 'tsk_mutation_table_truncate' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_truncate(tsk_mutation_table_t *self, tsk_size_t num_rows);
    ^                                                 ~~~~~
                                                      mutations
/home/benj/projects/tskit/c/build/../tskit/tables.c:2666:1: note: the definition seen here
tsk_mutation_table_truncate(tsk_mutation_table_t *mutations, tsk_size_t num_rows)
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1574:5: note: differing parameters are named here: ('self'), in definition: ('mutations')
int tsk_mutation_table_truncate(tsk_mutation_table_t *self, tsk_size_t num_rows);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1659:5: warning: function 'tsk_mutation_table_set_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_set_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2609:1: note: the definition seen here
tsk_mutation_table_set_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1659:5: note: differing parameters are named here: ('derived_state_length', 'metadata_length'), in definition: ('derived_state_offset', 'metadata_offset')
int tsk_mutation_table_set_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1662:5: warning: function 'tsk_mutation_table_append_columns' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_append_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:2505:1: note: the definition seen here
tsk_mutation_table_append_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1662:5: note: differing parameters are named here: ('derived_state_length', 'metadata_length'), in definition: ('derived_state_offset', 'metadata_offset')
int tsk_mutation_table_append_columns(tsk_mutation_table_t *self, tsk_size_t num_rows,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1667:5: warning: function 'tsk_mutation_table_truncate' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_mutation_table_truncate(tsk_mutation_table_t *self, tsk_size_t num_rows);
    ^                                                 ~~~~~
                                                      mutations
/home/benj/projects/tskit/c/build/../tskit/tables.c:2666:1: note: the definition seen here
tsk_mutation_table_truncate(tsk_mutation_table_t *mutations, tsk_size_t num_rows)
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1667:5: note: differing parameters are named here: ('self'), in definition: ('mutations')
int tsk_mutation_table_truncate(tsk_mutation_table_t *self, tsk_size_t num_rows);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1695:5: warning: function 'tsk_population_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_population_table_init(tsk_population_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3434:1: note: the definition seen here
tsk_population_table_init(tsk_population_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1695:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_population_table_init(tsk_population_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1854:5: warning: function 'tsk_provenance_table_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_provenance_table_init(tsk_provenance_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:3882:1: note: the definition seen here
tsk_provenance_table_init(tsk_provenance_table_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:1854:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_provenance_table_init(tsk_provenance_table_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2018:5: warning: function 'tsk_table_collection_init' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_init(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6695:1: note: the definition seen here
tsk_table_collection_init(tsk_table_collection_t *self, tsk_flags_t TSK_UNUSED(options))
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2018:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_init(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2189:5: warning: function 'tsk_table_collection_record_num_rows' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_record_num_rows(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7541:1: note: the definition seen here
tsk_table_collection_record_num_rows(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2189:5: note: differing parameters are named here: ('bookmark'), in definition: ('position')
int tsk_table_collection_record_num_rows(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2206:5: warning: function 'tsk_table_collection_truncate' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_truncate(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7556:1: note: the definition seen here
tsk_table_collection_truncate(tsk_table_collection_t *tables, tsk_bookmark_t *position)
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2206:5: note: differing parameters are named here: ('self', 'bookmark'), in definition: ('tables', 'position')
int tsk_table_collection_truncate(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2327:6: warning: function 'tsk_table_collection_has_index' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
bool tsk_table_collection_has_index(tsk_table_collection_t *self, tsk_flags_t options);
     ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6794:1: note: the definition seen here
tsk_table_collection_has_index(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2327:6: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
bool tsk_table_collection_has_index(tsk_table_collection_t *self, tsk_flags_t options);
     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2342:5: warning: function 'tsk_table_collection_drop_index' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_drop_index(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6802:1: note: the definition seen here
tsk_table_collection_drop_index(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2342:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_drop_index(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2357:5: warning: function 'tsk_table_collection_build_index' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_build_index(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:6813:1: note: the definition seen here
tsk_table_collection_build_index(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2357:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_build_index(tsk_table_collection_t *self, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2362:5: warning: function 'tsk_table_collection_link_ancestors' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_link_ancestors(tsk_table_collection_t *self, tsk_id_t *samples,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7289:1: note: the definition seen here
tsk_table_collection_link_ancestors(tsk_table_collection_t *self, tsk_id_t *samples,
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2362:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_link_ancestors(tsk_table_collection_t *self, tsk_id_t *samples,
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2366:5: warning: function 'tsk_table_collection_deduplicate_sites' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_deduplicate_sites(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7354:1: note: the definition seen here
tsk_table_collection_deduplicate_sites(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2366:5: note: differing parameters are named here: ('tables', 'options'), in definition: ('self', 'TSK_UNUSED_options')
int tsk_table_collection_deduplicate_sites(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2368:5: warning: function 'tsk_table_collection_compute_mutation_parents' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_table_collection_compute_mutation_parents(
    ^
/home/benj/projects/tskit/c/build/../tskit/tables.c:7426:1: note: the definition seen here
tsk_table_collection_compute_mutation_parents(
^
/home/benj/projects/tskit/c/build/../tskit/tables.h:2368:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_table_collection_compute_mutation_parents(
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/trees.c:181:18: warning: Result of 'calloc' is converted to a pointer of type 'tsk_size_t', which is incompatible with sizeof operand type 'size_t' [clang-analyzer-unix.MallocSizeof]
    node_count = calloc(TSK_MAX(1, num_inds), sizeof(size_t));
                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:181:18: note: Result of 'calloc' is converted to a pointer of type 'tsk_size_t', which is incompatible with sizeof operand type 'size_t'
/home/benj/projects/tskit/c/build/../tskit/trees.c:197:11: warning: Result of 'malloc' is converted to a pointer of type 'tsk_id_t', which is incompatible with sizeof operand type 'tsk_node_t' [clang-analyzer-unix.MallocSizeof]
        = malloc(TSK_MAX(1, total_node_refs) * sizeof(tsk_node_t));
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:197:11: note: Result of 'malloc' is converted to a pointer of type 'tsk_id_t', which is incompatible with sizeof operand type 'tsk_node_t'
/home/benj/projects/tskit/c/build/../tskit/trees.c:198:30: warning: Result of 'malloc' is converted to a pointer of type 'tsk_id_t *', which is incompatible with sizeof operand type 'tsk_node_t *' [clang-analyzer-unix.MallocSizeof]
    self->individual_nodes = malloc(TSK_MAX(1, num_inds) * sizeof(tsk_node_t *));
                             ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:198:30: note: Result of 'malloc' is converted to a pointer of type 'tsk_id_t *', which is incompatible with sizeof operand type 'tsk_node_t *'
/home/benj/projects/tskit/c/build/../tskit/trees.c:243:5: warning: Value stored to 'tree_right' is never read [clang-analyzer-deadcode.DeadStores]
    tree_right = sequence_length;
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:243:5: note: Value stored to 'tree_right' is never read
/home/benj/projects/tskit/c/build/../tskit/trees.c:331:21: warning: Call to 'malloc' has an allocation size of 0 bytes [clang-analyzer-unix.API]
    self->samples = malloc(self->num_samples * sizeof(tsk_id_t));
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2995:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2995:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3000:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3000:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3003:11: note: Calling 'tsk_treeseq_init'
    ret = tsk_treeseq_init(output, &tables, TSK_BUILD_INDEXES);
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:368:5: note: Taking false branch
    if (tables == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:373:9: note: Assuming the condition is false
    if (self->tables == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:373:5: note: Taking false branch
    if (self->tables == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:378:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:378:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:381:5: note: Taking true branch
    if (!!(options & TSK_BUILD_INDEXES)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:383:13: note: Assuming 'ret' is equal to 0
        if (ret != 0) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:383:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:388:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:388:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:400:9: note: Assuming the condition is false
    if (tables->file_uuid != NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:400:5: note: Taking false branch
    if (tables->file_uuid != NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:409:11: note: Calling 'tsk_treeseq_init_nodes'
    ret = tsk_treeseq_init_nodes(self);
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:325:17: note: Assuming 'j' is >= 'num_nodes'
    for (j = 0; j < num_nodes; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:325:5: note: Loop condition is false. Execution continues on line 331
    for (j = 0; j < num_nodes; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:331:21: note: Call to 'malloc' has an allocation size of 0 bytes
    self->samples = malloc(self->num_samples * sizeof(tsk_id_t));
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:381:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_BUILD_INDEXES)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:381:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_BUILD_INDEXES)) {
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:648:28: note: expanded from macro 'TSK_BUILD_INDEXES'
#define TSK_BUILD_INDEXES (1 << 0)
                           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:387:62: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_table_collection_check_integrity(self->tables, TSK_CHECK_ALL);
                                                             ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:642:39: note: expanded from macro 'TSK_CHECK_ALL'
        | TSK_CHECK_SITE_DUPLICATES | TSK_CHECK_MUTATION_ORDERING | TSK_CHECK_INDEXES)
                                      ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:638:38: note: expanded from macro 'TSK_CHECK_MUTATION_ORDERING'
#define TSK_CHECK_MUTATION_ORDERING (1 << 4)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:573:42: warning: macro argument should be enclosed in parentheses [misc-macro-parentheses]
#define GET_2D_ROW(array, row_len, row) (array + (((size_t)(row_len)) * (size_t) row))
                                         ^~~~~
                                         ()
/home/benj/projects/tskit/c/build/../tskit/trees.c:573:82: warning: macro argument should be enclosed in parentheses [misc-macro-parentheses]
#define GET_2D_ROW(array, row_len, row) (array + (((size_t)(row_len)) * (size_t) row))
                                                                                 ^~~~
                                                                                 ()
/home/benj/projects/tskit/c/build/../tskit/trees.c:604:76: warning: pointer parameter 'focal' can be pointer to const [readability-non-const-parameter]
tsk_treeseq_genealogical_nearest_neighbours(tsk_treeseq_t *self, tsk_id_t *focal,
                                                                 ~~~~~~~~  ^
                                                                 const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:605:58: warning: pointer parameter 'reference_set_size' can be pointer to const [readability-non-const-parameter]
    size_t num_focal, tsk_id_t **reference_sets, size_t *reference_set_size,
                                                 ~~~~~~  ^
                                                 const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:787:13: warning: pointer parameter 'reference_set_size' can be pointer to const [readability-non-const-parameter]
    size_t *reference_set_size, size_t num_reference_sets,
    ~~~~~~  ^
    const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:952:76: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
tsk_treeseq_check_windows(tsk_treeseq_t *self, size_t num_windows, double *windows)
                                                                   ~~~~~~  ^
                                                                   const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1018:33: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    size_t num_windows, double *windows, double *result, tsk_flags_t TSK_UNUSED(options))
                        ~~~~~~  ^
                        const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1299:33: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    size_t num_windows, double *windows, double *result, tsk_flags_t options)
                        ~~~~~~  ^
                        const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1329:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_POLARISED) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1329:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_POLARISED) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:54:38: note: expanded from macro 'TSK_STAT_POLARISED'
#define TSK_STAT_POLARISED          (1 << 10)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1419:57: warning: pointer parameter 'source' can be pointer to const [readability-non-const-parameter]
increment_row(size_t length, double multiplier, double *source, double *dest)
                                                ~~~~~~  ^
                                                const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1431:33: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    size_t num_windows, double *windows, double *result, tsk_flags_t TSK_UNUSED(options))
                        ~~~~~~  ^
                        const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1559:44: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
span_normalise(size_t num_windows, double *windows, size_t row_size, double *array)
                                   ~~~~~~  ^
                                   const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1622:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1622:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:50:38: note: expanded from macro 'TSK_STAT_BRANCH'
#define TSK_STAT_BRANCH             (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1623:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = options & TSK_STAT_POLARISED;
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1623:32: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = options & TSK_STAT_POLARISED;
                               ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:54:38: note: expanded from macro 'TSK_STAT_POLARISED'
#define TSK_STAT_POLARISED          (1 << 10)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1648:40: warning: Assigned value is garbage or undefined [clang-analyzer-core.uninitialized.Assign]
                upargs.total_weight[k] += weight_u[k];
                                       ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2347:27: note: Storing uninitialized value
    double *new_weights = malloc((num_weights + 1) * num_samples * sizeof(double));
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2350:9: note: Assuming 'new_weights' is not equal to NULL
    if (new_weights == NULL || means == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2350:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:2350:32: note: Assuming 'means' is not equal to NULL
    if (new_weights == NULL || means == NULL) {
                               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2350:5: note: Taking false branch
    if (new_weights == NULL || means == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2356:17: note: Assuming 'j' is >= 'num_samples'
    for (j = 0; j < num_samples; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2356:5: note: Loop condition is false. Execution continues on line 2362
    for (j = 0; j < num_samples; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2362:5: note: Loop condition is true.  Entering loop body
    for (k = 0; k < num_weights; k++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2362:17: note: Assuming 'k' is >= 'num_weights'
    for (k = 0; k < num_weights; k++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2362:5: note: Loop condition is false. Execution continues on line 2365
    for (k = 0; k < num_weights; k++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2365:5: note: Loop condition is false. Execution continues on line 2373
    for (j = 0; j < num_samples; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2373:11: note: Calling 'tsk_treeseq_general_stat'
    ret = tsk_treeseq_general_stat(self, num_weights, new_weights, num_weights,
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1677:23: note: Assuming the condition is true
    bool stat_site = !!(options & TSK_STAT_SITE);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1678:25: note: Assuming the condition is false
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1679:23: note: Assuming the condition is true
    bool stat_node = !!(options & TSK_STAT_NODE);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1684:11: note: Left side of '||' is false
    if (!(stat_site || stat_branch || stat_node)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1684:36: note: Left side of '||' is true
    if (!(stat_site || stat_branch || stat_node)) {
                                   ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1684:5: note: Taking false branch
    if (!(stat_site || stat_branch || stat_node)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1688:5: note: Taking false branch
    if (stat_site + stat_branch + stat_node > 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1693:5: note: Taking false branch
    if (state_dim < 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1697:5: note: Taking false branch
    if (result_dim < 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1701:9: note: Assuming 'windows' is not equal to NULL
    if (windows == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1701:5: note: Taking false branch
    if (windows == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1706:13: note: Assuming 'ret' is equal to 0
        if (ret != 0) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1706:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1711:5: note: Taking false branch
    if (stat_site) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1715:15: note: Calling 'tsk_polarisable_func_general_stat'
        ret = tsk_polarisable_func_general_stat(self, state_dim, sample_weights,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1631:9: note: Assuming 'polarised' is 0
    if (!polarised) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1631:5: note: Taking true branch
    if (!polarised) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:13: note: Assuming the condition is false
        if (upargs.total_weight == NULL || upargs.total_minus_state == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:44: note: Assuming the condition is false
        if (upargs.total_weight == NULL || upargs.total_minus_state == NULL
                                           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:13: note: Left side of '||' is false
        if (upargs.total_weight == NULL || upargs.total_minus_state == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1639:16: note: Assuming the condition is false
            || upargs.result_tmp == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:9: note: Taking false branch
        if (upargs.total_weight == NULL || upargs.total_minus_state == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1645:21: note: Assuming the condition is true
        for (j = 0; j < self->num_samples; j++) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1645:9: note: Loop condition is true.  Entering loop body
        for (j = 0; j < self->num_samples; j++) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1647:13: note: Loop condition is true.  Entering loop body
            for (k = 0; k < state_dim; k++) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1648:40: note: Assigned value is garbage or undefined
                upargs.total_weight[k] += weight_u[k];
                                       ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1677:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_site = !!(options & TSK_STAT_SITE);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1677:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_site = !!(options & TSK_STAT_SITE);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:49:38: note: expanded from macro 'TSK_STAT_SITE'
#define TSK_STAT_SITE               (1 << 0)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1678:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1678:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:50:38: note: expanded from macro 'TSK_STAT_BRANCH'
#define TSK_STAT_BRANCH             (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1679:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_node = !!(options & TSK_STAT_NODE);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1679:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_node = !!(options & TSK_STAT_NODE);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:51:38: note: expanded from macro 'TSK_STAT_NODE'
#define TSK_STAT_NODE               (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1719:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_SPAN_NORMALISE) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1719:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_SPAN_NORMALISE) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:55:38: note: expanded from macro 'TSK_STAT_SPAN_NORMALISE'
#define TSK_STAT_SPAN_NORMALISE     (1 << 11)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1732:78: warning: pointer parameter 'set_indexes' can be pointer to const [readability-non-const-parameter]
check_set_indexes(tsk_size_t num_sets, tsk_size_t num_set_indexes, tsk_id_t *set_indexes)
                                                                   ~~~~~~~~  ^
                                                                   const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1749:17: warning: pointer parameter 'sample_set_sizes' can be pointer to const [readability-non-const-parameter]
    tsk_size_t *sample_set_sizes, tsk_id_t *sample_sets)
    ~~~~~~~~~~  ^
    const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1749:45: warning: pointer parameter 'sample_sets' can be pointer to const [readability-non-const-parameter]
    tsk_size_t *sample_set_sizes, tsk_id_t *sample_sets)
                                  ~~~~~~~~  ^
                                  const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1804:15: warning: pointer parameter 'set_indexes' can be pointer to const [readability-non-const-parameter]
    tsk_id_t *set_indexes, general_stat_func_t *f, tsk_size_t num_windows,
    ~~~~~~~~  ^
    const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1891:30: warning: Call to 'malloc' has an allocation size of 0 bytes [clang-analyzer-unix.API]
    tsk_size_t *coordinate = malloc(num_sample_sets * sizeof(*coordinate));
                             ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2201:23: note: Assuming the condition is false
    bool stat_site = !!(options & TSK_STAT_SITE);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2202:25: note: Assuming the condition is true
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2203:23: note: Assuming the condition is true
    bool stat_node = !!(options & TSK_STAT_NODE);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2215:5: note: Taking false branch
    if (stat_node) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2220:21: note: Left side of '||' is true
    if (!(stat_site || stat_branch)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2220:5: note: Taking false branch
    if (!(stat_site || stat_branch)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2224:5: note: Taking false branch
    if (stat_site + stat_branch > 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2228:9: note: Assuming 'windows' is not equal to NULL
    if (windows == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2228:5: note: Taking false branch
    if (windows == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2233:13: note: Assuming 'ret' is equal to 0
        if (ret != 0) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2233:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2239:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2239:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2246:9: note: Assuming 'counts' is not equal to NULL
    if (counts == NULL || result_dims == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2246:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:2246:27: note: Assuming 'result_dims' is not equal to NULL
    if (counts == NULL || result_dims == NULL) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2246:5: note: Taking false branch
    if (counts == NULL || result_dims == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2252:17: note: Assuming 'k' is >= 'num_sample_sets'
    for (k = 0; k < num_sample_sets; k++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2252:5: note: Loop condition is false. Execution continues on line 2266
    for (k = 0; k < num_sample_sets; k++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2266:17: note: Assuming the condition is false
    for (j = 0; j < self->num_samples; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2266:5: note: Loop condition is false. Execution continues on line 2271
    for (j = 0; j < self->num_samples; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2274:5: note: Taking true branch
    if (stat_site) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2275:15: note: Calling 'tsk_treeseq_site_allele_frequency_spectrum'
        ret = tsk_treeseq_site_allele_frequency_spectrum(self, num_sample_sets,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1956:9: note: Assuming 'parent' is not equal to NULL
    if (parent == NULL || total_counts == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1956:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:1956:27: note: Assuming 'total_counts' is not equal to NULL
    if (parent == NULL || total_counts == NULL) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1956:5: note: Taking false branch
    if (parent == NULL || total_counts == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1962:5: note: Loop condition is false. Execution continues on line 1965
    for (j = 0; j < num_sample_sets; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1973:12: note: Assuming 'tj' is >= 'num_edges'
    while (tj < num_edges || t_left < sequence_length) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1973:12: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:1973:5: note: Loop condition is true.  Entering loop body
    while (tj < num_edges || t_left < sequence_length) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1974:31: note: Left side of '&&' is false
        while (tk < num_edges && edge_right[O[tk]] == t_left) {
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1986:31: note: Left side of '&&' is false
        while (tj < num_edges && edge_left[I[tj]] == t_left) {
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1998:9: note: Taking false branch
        if (tj < num_edges) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2001:9: note: Taking false branch
        if (tk < num_edges) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2006:29: note: Assuming the condition is true
        for (tree_site = 0; tree_site < self->tree_sites_length[tree_index];
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2006:9: note: Loop condition is true.  Entering loop body
        for (tree_site = 0; tree_site < self->tree_sites_length[tree_index];
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2009:13: note: Loop condition is false. Execution continues on line 2013
            while (windows[window_index + 1] <= site->position) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2013:19: note: Calling 'tsk_treeseq_update_site_afs'
            ret = tsk_treeseq_update_site_afs(self, site, total_counts, counts,
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1891:30: note: Call to 'malloc' has an allocation size of 0 bytes
    tsk_size_t *coordinate = malloc(num_sample_sets * sizeof(*coordinate));
                             ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1892:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = !!(options & TSK_STAT_POLARISED);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1892:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = !!(options & TSK_STAT_POLARISED);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:54:38: note: expanded from macro 'TSK_STAT_POLARISED'
#define TSK_STAT_POLARISED          (1 << 10)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1933:37: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    tsk_size_t num_windows, double *windows, tsk_size_t *result_dims, double *result,
                            ~~~~~~  ^
                            const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2044:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = !!(options & TSK_STAT_POLARISED);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2044:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = !!(options & TSK_STAT_POLARISED);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:54:38: note: expanded from macro 'TSK_STAT_POLARISED'
#define TSK_STAT_POLARISED          (1 << 10)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2076:81: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    tsk_size_t num_sample_sets, double *counts, tsk_size_t num_windows, double *windows,
                                                                        ~~~~~~  ^
                                                                        const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2201:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_site = !!(options & TSK_STAT_SITE);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2201:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_site = !!(options & TSK_STAT_SITE);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:49:38: note: expanded from macro 'TSK_STAT_SITE'
#define TSK_STAT_SITE               (1 << 0)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2202:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2202:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:50:38: note: expanded from macro 'TSK_STAT_BRANCH'
#define TSK_STAT_BRANCH             (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2203:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_node = !!(options & TSK_STAT_NODE);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2203:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_node = !!(options & TSK_STAT_NODE);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:51:38: note: expanded from macro 'TSK_STAT_NODE'
#define TSK_STAT_NODE               (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2283:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_SPAN_NORMALISE) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2283:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_SPAN_NORMALISE) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:55:38: note: expanded from macro 'TSK_STAT_SPAN_NORMALISE'
#define TSK_STAT_SPAN_NORMALISE     (1 << 11)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2297:50: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
diversity_summary_func(size_t state_dim, double *state, size_t TSK_UNUSED(result_dim),
                                         ~~~~~~  ^
                                         const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2323:57: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
trait_covariance_summary_func(size_t state_dim, double *state,
                                                ~~~~~~  ^
                                                const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2383:58: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
trait_correlation_summary_func(size_t state_dim, double *state,
                                                 ~~~~~~  ^
                                                 const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2465:31: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
    size_t state_dim, double *state, size_t result_dim, double *result, void *params)
                      ~~~~~~  ^
                      const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2577:58: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
segregating_sites_summary_func(size_t state_dim, double *state,
                                                 ~~~~~~  ^
                                                 const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2604:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
Y1_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2659:63: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
divergence_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                                      ~~~~~~  ^
                                                      const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2698:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
Y2_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2737:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
f2_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2782:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
Y3_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2824:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
f3_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2871:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
f4_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:3003:45: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_treeseq_init(output, &tables, TSK_BUILD_INDEXES);
                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:648:28: note: expanded from macro 'TSK_BUILD_INDEXES'
#define TSK_BUILD_INDEXES (1 << 0)
                           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3021:34: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const bool sample_counts = !(self->options & TSK_NO_SAMPLE_COUNTS);
                                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3021:50: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const bool sample_counts = !(self->options & TSK_NO_SAMPLE_COUNTS);
                                                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3022:34: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const bool sample_lists = !!(self->options & TSK_SAMPLE_LISTS);
                                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3022:50: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const bool sample_lists = !!(self->options & TSK_SAMPLE_LISTS);
                                                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:9: warning: Potential memory leak [clang-analyzer-unix.Malloc]
    if (options & TSK_SAMPLE_COUNTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3108:25: note: Memory is allocated
    self->right_child = malloc(num_nodes * sizeof(tsk_id_t));
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:42: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3136:16: note: Assuming the condition is false
            || self->next_sample == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:9: note: Taking false branch
        if (self->left_sample == NULL || self->right_sample == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Returned allocated memory
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:9: note: Potential memory leak
    if (options & TSK_SAMPLE_COUNTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_SAMPLE_COUNTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_SAMPLE_COUNTS) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:45:38: note: expanded from macro 'TSK_SAMPLE_COUNTS'
#define TSK_SAMPLE_COUNTS           (1 << 0)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3134:29: warning: Call to 'malloc' has an allocation size of 0 bytes [clang-analyzer-unix.API]
        self->next_sample = malloc(num_samples * sizeof(*self->next_sample));
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3134:29: note: Call to 'malloc' has an allocation size of 0 bytes
        self->next_sample = malloc(num_samples * sizeof(*self->next_sample));
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3193:15: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !!(self->options & TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3193:31: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !!(self->options & TSK_SAMPLE_LISTS);
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3199:14: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !(self->options & TSK_NO_SAMPLE_COUNTS);
             ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3199:30: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !(self->options & TSK_NO_SAMPLE_COUNTS);
                             ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3218:61: warning: pointer parameter 'tracked_samples' can be pointer to const [readability-non-const-parameter]
    tsk_tree_t *self, size_t num_tracked_samples, tsk_id_t *tracked_samples)
                                                  ~~~~~~~~  ^
                                                  const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:3303:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3329:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(dest->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3329:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(dest->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3330:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (self->options & TSK_NO_SAMPLE_COUNTS) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3330:29: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (self->options & TSK_NO_SAMPLE_COUNTS) {
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3339:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (dest->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3339:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (dest->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3340:15: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (!(self->options & TSK_SAMPLE_LISTS)) {
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3340:31: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (!(self->options & TSK_SAMPLE_LISTS)) {
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3478:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3478:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3497:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_NO_SAMPLE_COUNTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3497:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_NO_SAMPLE_COUNTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3669:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3669:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3681:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3681:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3709:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3709:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3718:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (self->options & TSK_SAMPLE_LISTS) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3718:29: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (self->options & TSK_SAMPLE_LISTS) {
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3721:15: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3721:31: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3808:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3808:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3852:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3852:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: warning: Potential leak of memory pointed to by 'left_child' [clang-analyzer-unix.Malloc]
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3107:24: note: Memory is allocated
    self->left_child = malloc(num_nodes * sizeof(tsk_id_t));
                       ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:42: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3136:16: note: Assuming the condition is false
            || self->next_sample == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:9: note: Taking false branch
        if (self->left_sample == NULL || self->right_sample == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Returned allocated memory
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is false. Execution continues on line 4935
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4939:5: note: Taking false branch
    if (ret != 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4943:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4950:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4953:19: note: Calling 'tsk_tree_next'
    while ((ret = tsk_tree_next(&trees[1])) == 1) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4122:5: note: Taking true branch
    if (self->index == -1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4123:15: note: Calling 'tsk_tree_first'
        ret = tsk_tree_first(self);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:9: note: Assuming the condition is true
    if (tables->edges.num_rows > 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:5: note: Taking true branch
    if (tables->edges.num_rows > 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4060:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4069:15: note: Calling 'tsk_tree_advance'
        ret = tsk_tree_advance(self, TSK_DIR_FORWARD, tables->edges.right,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3978:5: note: Taking true branch
    if (direction == TSK_DIR_FORWARD) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:5: note: Loop condition is false. Execution continues on line 3993
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:5: note: Loop condition is true.  Entering loop body
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3996:15: note: Calling 'tsk_tree_insert_edge'
        ret = tsk_tree_insert_edge(self, edge_parent[k], edge_child[k]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3878:5: note: Taking false branch
    if (parent[c] != TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:9: note: Assuming the condition is false
    if (u == TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:5: note: Taking false branch
    if (u == TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:16: note: Assuming the condition is false
        while (u != TSK_NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:9: note: Loop condition is false. Execution continues on line 3913
        while (u != TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3913:9: note: Taking false branch
        if (IS_ROOT(c)) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3938:35: note: Left side of '&&' is false
            if (IS_ROOT(path_end) && !path_end_was_root) {
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: note: Potential leak of memory pointed to by 'left_child'
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: warning: Potential leak of memory pointed to by 'parent' [clang-analyzer-unix.Malloc]
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3106:20: note: Memory is allocated
    self->parent = malloc(num_nodes * sizeof(tsk_id_t));
                   ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:42: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3136:16: note: Assuming the condition is false
            || self->next_sample == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:9: note: Taking false branch
        if (self->left_sample == NULL || self->right_sample == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Returned allocated memory
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is false. Execution continues on line 4935
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4939:5: note: Taking false branch
    if (ret != 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4943:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4950:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4953:19: note: Calling 'tsk_tree_next'
    while ((ret = tsk_tree_next(&trees[1])) == 1) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4122:5: note: Taking true branch
    if (self->index == -1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4123:15: note: Calling 'tsk_tree_first'
        ret = tsk_tree_first(self);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:9: note: Assuming the condition is true
    if (tables->edges.num_rows > 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:5: note: Taking true branch
    if (tables->edges.num_rows > 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4060:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4069:15: note: Calling 'tsk_tree_advance'
        ret = tsk_tree_advance(self, TSK_DIR_FORWARD, tables->edges.right,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3978:5: note: Taking true branch
    if (direction == TSK_DIR_FORWARD) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:5: note: Loop condition is false. Execution continues on line 3993
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:5: note: Loop condition is true.  Entering loop body
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3996:15: note: Calling 'tsk_tree_insert_edge'
        ret = tsk_tree_insert_edge(self, edge_parent[k], edge_child[k]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3878:5: note: Taking false branch
    if (parent[c] != TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:9: note: Assuming the condition is false
    if (u == TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:5: note: Taking false branch
    if (u == TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:16: note: Assuming the condition is false
        while (u != TSK_NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:9: note: Loop condition is false. Execution continues on line 3913
        while (u != TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3913:9: note: Taking false branch
        if (IS_ROOT(c)) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3938:35: note: Left side of '&&' is false
            if (IS_ROOT(path_end) && !path_end_was_root) {
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: note: Potential leak of memory pointed to by 'parent'
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: warning: Potential leak of memory pointed to by 'right_sib' [clang-analyzer-unix.Malloc]
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3110:23: note: Memory is allocated
    self->right_sib = malloc(num_nodes * sizeof(tsk_id_t));
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:42: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3136:16: note: Assuming the condition is false
            || self->next_sample == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:9: note: Taking false branch
        if (self->left_sample == NULL || self->right_sample == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Returned allocated memory
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is false. Execution continues on line 4935
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4939:5: note: Taking false branch
    if (ret != 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4943:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4950:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4953:19: note: Calling 'tsk_tree_next'
    while ((ret = tsk_tree_next(&trees[1])) == 1) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4122:5: note: Taking true branch
    if (self->index == -1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4123:15: note: Calling 'tsk_tree_first'
        ret = tsk_tree_first(self);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:9: note: Assuming the condition is true
    if (tables->edges.num_rows > 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:5: note: Taking true branch
    if (tables->edges.num_rows > 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4060:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4069:15: note: Calling 'tsk_tree_advance'
        ret = tsk_tree_advance(self, TSK_DIR_FORWARD, tables->edges.right,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3978:5: note: Taking true branch
    if (direction == TSK_DIR_FORWARD) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:5: note: Loop condition is false. Execution continues on line 3993
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:5: note: Loop condition is true.  Entering loop body
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3996:15: note: Calling 'tsk_tree_insert_edge'
        ret = tsk_tree_insert_edge(self, edge_parent[k], edge_child[k]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3878:5: note: Taking false branch
    if (parent[c] != TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:9: note: Assuming the condition is false
    if (u == TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:5: note: Taking false branch
    if (u == TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:16: note: Assuming the condition is false
        while (u != TSK_NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:9: note: Loop condition is false. Execution continues on line 3913
        while (u != TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3913:9: note: Taking false branch
        if (IS_ROOT(c)) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3938:35: note: Left side of '&&' is false
            if (IS_ROOT(path_end) && !path_end_was_root) {
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: note: Potential leak of memory pointed to by 'right_sib'
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4157:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return value | (1ULL << bit);
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4163:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return (value & (1ULL << bit)) != 0;
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4348:23: warning: Potential memory leak [clang-analyzer-unix.Malloc]
    self->num_nodes = tsk_treeseq_get_num_nodes(tree_sequence);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4925:15: note: Calling 'tsk_diff_iter_init'
        ret = tsk_diff_iter_init(&diff_iters[i], treeseqs[i]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4355:29: note: Memory is allocated
    self->edge_list_nodes = malloc(self->num_edges * sizeof(*self->edge_list_nodes));
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4356:9: note: Assuming the condition is false
    if (self->edge_list_nodes == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4356:5: note: Taking false branch
    if (self->edge_list_nodes == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4925:15: note: Returned allocated memory
        ret = tsk_diff_iter_init(&diff_iters[i], treeseqs[i]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4925:15: note: Calling 'tsk_diff_iter_init'
        ret = tsk_diff_iter_init(&diff_iters[i], treeseqs[i]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4348:23: note: Potential memory leak
    self->num_nodes = tsk_treeseq_get_num_nodes(tree_sequence);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4506:22: warning: either cast from 'int' to 'size_t' (aka 'unsigned long') is ineffective, or there is loss of precision before the conversion [misc-misplaced-widening-cast]
    self->m = calloc((size_t)(self->N + self->n), sizeof(tsk_size_t));
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4507:22: warning: either cast from 'int' to 'size_t' (aka 'unsigned long') is ineffective, or there is loss of precision before the conversion [misc-misplaced-widening-cast]
    self->M = calloc((size_t)(self->N + self->n), sizeof(double));
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4826:17: warning: redundant cast to the same type [google-readability-casting]
        depth = (tsk_size_t) stack[stack_top].depth;
                ^~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:53: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
                                                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:225:5: warning: function 'tsk_treeseq_load' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_treeseq_load(tsk_treeseq_t *self, const char *filename, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:437:1: note: the definition seen here
tsk_treeseq_load(
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:225:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_treeseq_load(tsk_treeseq_t *self, const char *filename, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:275:5: warning: function 'tsk_treeseq_genealogical_nearest_neighbours' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_treeseq_genealogical_nearest_neighbours(tsk_treeseq_t *self, tsk_id_t *focal,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:604:1: note: the definition seen here
tsk_treeseq_genealogical_nearest_neighbours(tsk_treeseq_t *self, tsk_id_t *focal,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:275:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_treeseq_genealogical_nearest_neighbours(tsk_treeseq_t *self, tsk_id_t *focal,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:278:5: warning: function 'tsk_treeseq_mean_descendants' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_treeseq_mean_descendants(tsk_treeseq_t *self, tsk_id_t **reference_sets,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:786:1: note: the definition seen here
tsk_treeseq_mean_descendants(tsk_treeseq_t *self, tsk_id_t **reference_sets,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:278:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_treeseq_mean_descendants(tsk_treeseq_t *self, tsk_id_t **reference_sets,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:286:5: warning: function 'tsk_treeseq_general_stat' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_treeseq_general_stat(tsk_treeseq_t *self, size_t K, double *W, size_t M,
    ^                                                    ~~         ~~        ~~
                                                         state_dim  sample_weights result_dim
/home/benj/projects/tskit/c/build/../tskit/trees.c:1672:1: note: the definition seen here
tsk_treeseq_general_stat(tsk_treeseq_t *self, size_t state_dim, double *sample_weights,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:286:5: note: differing parameters are named here: ('K', 'W', 'M', 'sigma'), in definition: ('state_dim', 'sample_weights', 'result_dim', 'result')
int tsk_treeseq_general_stat(tsk_treeseq_t *self, size_t K, double *W, size_t M,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:393:5: warning: function 'tsk_tree_depth' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_tree_depth(tsk_tree_t *self, tsk_id_t u, tsk_size_t *depth);
    ^                                                        ~~~~~~
                                                             depth_ret
/home/benj/projects/tskit/c/build/../tskit/trees.c:3584:1: note: the definition seen here
tsk_tree_depth(tsk_tree_t *self, tsk_id_t u, tsk_size_t *depth_ret)
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:393:5: note: differing parameters are named here: ('depth'), in definition: ('depth_ret')
int tsk_tree_depth(tsk_tree_t *self, tsk_id_t u, tsk_size_t *depth);
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:401:5: warning: function 'tsk_tree_map_mutations' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_tree_map_mutations(tsk_tree_t *self, int8_t *genotypes, double *cost_matrix,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4188:1: note: the definition seen here
tsk_tree_map_mutations(tsk_tree_t *self, int8_t *genotypes,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:401:5: note: differing parameters are named here: ('cost_matrix', 'options', 'ancestral_state', 'num_transitions', 'transitions'), in definition: ('TSK_UNUSED_cost_matrix', 'TSK_UNUSED_options', 'r_ancestral_state', 'r_num_transitions', 'r_transitions')
int tsk_tree_map_mutations(tsk_tree_t *self, int8_t *genotypes, double *cost_matrix,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:414:5: warning: function 'tsk_diff_iter_next' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_diff_iter_next(tsk_diff_iter_t *self, double *left, double *right,
    ^                                                 ~~~~~         ~~~~~~
                                                      ret_left      ret_right
/home/benj/projects/tskit/c/build/../tskit/trees.c:4383:1: note: the definition seen here
tsk_diff_iter_next(tsk_diff_iter_t *self, double *ret_left, double *ret_right,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:414:5: note: differing parameters are named here: ('left', 'right', 'edges_out', 'edges_in'), in definition: ('ret_left', 'ret_right', 'edges_out_ret', 'edges_in_ret')
int tsk_diff_iter_next(tsk_diff_iter_t *self, double *left, double *right,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:26:1: warning: #includes are not sorted properly [llvm-include-order]
#include <stdio.h>
^        ~~~~~~~~~
         <assert.h>
/home/benj/projects/tskit/c/build/../tskit/trees.c:181:18: warning: Result of 'calloc' is converted to a pointer of type 'tsk_size_t', which is incompatible with sizeof operand type 'size_t' [clang-analyzer-unix.MallocSizeof]
    node_count = calloc(TSK_MAX(1, num_inds), sizeof(size_t));
                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:181:18: note: Result of 'calloc' is converted to a pointer of type 'tsk_size_t', which is incompatible with sizeof operand type 'size_t'
/home/benj/projects/tskit/c/build/../tskit/trees.c:197:11: warning: Result of 'malloc' is converted to a pointer of type 'tsk_id_t', which is incompatible with sizeof operand type 'tsk_node_t' [clang-analyzer-unix.MallocSizeof]
        = malloc(TSK_MAX(1, total_node_refs) * sizeof(tsk_node_t));
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:197:11: note: Result of 'malloc' is converted to a pointer of type 'tsk_id_t', which is incompatible with sizeof operand type 'tsk_node_t'
/home/benj/projects/tskit/c/build/../tskit/trees.c:198:30: warning: Result of 'malloc' is converted to a pointer of type 'tsk_id_t *', which is incompatible with sizeof operand type 'tsk_node_t *' [clang-analyzer-unix.MallocSizeof]
    self->individual_nodes = malloc(TSK_MAX(1, num_inds) * sizeof(tsk_node_t *));
                             ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:198:30: note: Result of 'malloc' is converted to a pointer of type 'tsk_id_t *', which is incompatible with sizeof operand type 'tsk_node_t *'
/home/benj/projects/tskit/c/build/../tskit/trees.c:243:5: warning: Value stored to 'tree_right' is never read [clang-analyzer-deadcode.DeadStores]
    tree_right = sequence_length;
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:243:5: note: Value stored to 'tree_right' is never read
/home/benj/projects/tskit/c/build/../tskit/trees.c:331:21: warning: Call to 'malloc' has an allocation size of 0 bytes [clang-analyzer-unix.API]
    self->samples = malloc(self->num_samples * sizeof(tsk_id_t));
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2995:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2995:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3000:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3000:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3003:11: note: Calling 'tsk_treeseq_init'
    ret = tsk_treeseq_init(output, &tables, TSK_BUILD_INDEXES);
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:368:5: note: Taking false branch
    if (tables == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:373:9: note: Assuming the condition is false
    if (self->tables == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:373:5: note: Taking false branch
    if (self->tables == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:378:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:378:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:381:5: note: Taking true branch
    if (!!(options & TSK_BUILD_INDEXES)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:383:13: note: Assuming 'ret' is equal to 0
        if (ret != 0) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:383:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:388:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:388:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:400:9: note: Assuming the condition is false
    if (tables->file_uuid != NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:400:5: note: Taking false branch
    if (tables->file_uuid != NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:409:11: note: Calling 'tsk_treeseq_init_nodes'
    ret = tsk_treeseq_init_nodes(self);
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:325:17: note: Assuming 'j' is >= 'num_nodes'
    for (j = 0; j < num_nodes; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:325:5: note: Loop condition is false. Execution continues on line 331
    for (j = 0; j < num_nodes; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:331:21: note: Call to 'malloc' has an allocation size of 0 bytes
    self->samples = malloc(self->num_samples * sizeof(tsk_id_t));
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:381:12: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_BUILD_INDEXES)) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:381:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!!(options & TSK_BUILD_INDEXES)) {
                     ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:648:28: note: expanded from macro 'TSK_BUILD_INDEXES'
#define TSK_BUILD_INDEXES (1 << 0)
                           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:387:62: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_table_collection_check_integrity(self->tables, TSK_CHECK_ALL);
                                                             ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:642:39: note: expanded from macro 'TSK_CHECK_ALL'
        | TSK_CHECK_SITE_DUPLICATES | TSK_CHECK_MUTATION_ORDERING | TSK_CHECK_INDEXES)
                                      ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:638:38: note: expanded from macro 'TSK_CHECK_MUTATION_ORDERING'
#define TSK_CHECK_MUTATION_ORDERING (1 << 4)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:573:42: warning: macro argument should be enclosed in parentheses [misc-macro-parentheses]
#define GET_2D_ROW(array, row_len, row) (array + (((size_t)(row_len)) * (size_t) row))
                                         ^~~~~
                                         ()
/home/benj/projects/tskit/c/build/../tskit/trees.c:573:82: warning: macro argument should be enclosed in parentheses [misc-macro-parentheses]
#define GET_2D_ROW(array, row_len, row) (array + (((size_t)(row_len)) * (size_t) row))
                                                                                 ^~~~
                                                                                 ()
/home/benj/projects/tskit/c/build/../tskit/trees.c:604:76: warning: pointer parameter 'focal' can be pointer to const [readability-non-const-parameter]
tsk_treeseq_genealogical_nearest_neighbours(tsk_treeseq_t *self, tsk_id_t *focal,
                                                                 ~~~~~~~~  ^
                                                                 const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:605:58: warning: pointer parameter 'reference_set_size' can be pointer to const [readability-non-const-parameter]
    size_t num_focal, tsk_id_t **reference_sets, size_t *reference_set_size,
                                                 ~~~~~~  ^
                                                 const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:787:13: warning: pointer parameter 'reference_set_size' can be pointer to const [readability-non-const-parameter]
    size_t *reference_set_size, size_t num_reference_sets,
    ~~~~~~  ^
    const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:952:76: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
tsk_treeseq_check_windows(tsk_treeseq_t *self, size_t num_windows, double *windows)
                                                                   ~~~~~~  ^
                                                                   const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1018:33: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    size_t num_windows, double *windows, double *result, tsk_flags_t TSK_UNUSED(options))
                        ~~~~~~  ^
                        const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1299:33: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    size_t num_windows, double *windows, double *result, tsk_flags_t options)
                        ~~~~~~  ^
                        const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1329:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_POLARISED) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1329:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_POLARISED) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:54:38: note: expanded from macro 'TSK_STAT_POLARISED'
#define TSK_STAT_POLARISED          (1 << 10)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1419:57: warning: pointer parameter 'source' can be pointer to const [readability-non-const-parameter]
increment_row(size_t length, double multiplier, double *source, double *dest)
                                                ~~~~~~  ^
                                                const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1431:33: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    size_t num_windows, double *windows, double *result, tsk_flags_t TSK_UNUSED(options))
                        ~~~~~~  ^
                        const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1559:44: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
span_normalise(size_t num_windows, double *windows, size_t row_size, double *array)
                                   ~~~~~~  ^
                                   const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1622:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1622:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:50:38: note: expanded from macro 'TSK_STAT_BRANCH'
#define TSK_STAT_BRANCH             (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1623:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = options & TSK_STAT_POLARISED;
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1623:32: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = options & TSK_STAT_POLARISED;
                               ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:54:38: note: expanded from macro 'TSK_STAT_POLARISED'
#define TSK_STAT_POLARISED          (1 << 10)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1648:40: warning: Assigned value is garbage or undefined [clang-analyzer-core.uninitialized.Assign]
                upargs.total_weight[k] += weight_u[k];
                                       ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2347:27: note: Storing uninitialized value
    double *new_weights = malloc((num_weights + 1) * num_samples * sizeof(double));
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2350:9: note: Assuming 'new_weights' is not equal to NULL
    if (new_weights == NULL || means == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2350:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:2350:32: note: Assuming 'means' is not equal to NULL
    if (new_weights == NULL || means == NULL) {
                               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2350:5: note: Taking false branch
    if (new_weights == NULL || means == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2356:17: note: Assuming 'j' is >= 'num_samples'
    for (j = 0; j < num_samples; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2356:5: note: Loop condition is false. Execution continues on line 2362
    for (j = 0; j < num_samples; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2362:5: note: Loop condition is true.  Entering loop body
    for (k = 0; k < num_weights; k++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2362:17: note: Assuming 'k' is >= 'num_weights'
    for (k = 0; k < num_weights; k++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2362:5: note: Loop condition is false. Execution continues on line 2365
    for (k = 0; k < num_weights; k++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2365:5: note: Loop condition is false. Execution continues on line 2373
    for (j = 0; j < num_samples; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2373:11: note: Calling 'tsk_treeseq_general_stat'
    ret = tsk_treeseq_general_stat(self, num_weights, new_weights, num_weights,
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1677:23: note: Assuming the condition is true
    bool stat_site = !!(options & TSK_STAT_SITE);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1678:25: note: Assuming the condition is false
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1679:23: note: Assuming the condition is true
    bool stat_node = !!(options & TSK_STAT_NODE);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1684:11: note: Left side of '||' is false
    if (!(stat_site || stat_branch || stat_node)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1684:36: note: Left side of '||' is true
    if (!(stat_site || stat_branch || stat_node)) {
                                   ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1684:5: note: Taking false branch
    if (!(stat_site || stat_branch || stat_node)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1688:5: note: Taking false branch
    if (stat_site + stat_branch + stat_node > 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1693:5: note: Taking false branch
    if (state_dim < 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1697:5: note: Taking false branch
    if (result_dim < 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1701:9: note: Assuming 'windows' is not equal to NULL
    if (windows == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1701:5: note: Taking false branch
    if (windows == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1706:13: note: Assuming 'ret' is equal to 0
        if (ret != 0) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1706:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1711:5: note: Taking false branch
    if (stat_site) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1715:15: note: Calling 'tsk_polarisable_func_general_stat'
        ret = tsk_polarisable_func_general_stat(self, state_dim, sample_weights,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1631:9: note: Assuming 'polarised' is 0
    if (!polarised) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1631:5: note: Taking true branch
    if (!polarised) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:13: note: Assuming the condition is false
        if (upargs.total_weight == NULL || upargs.total_minus_state == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:44: note: Assuming the condition is false
        if (upargs.total_weight == NULL || upargs.total_minus_state == NULL
                                           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:13: note: Left side of '||' is false
        if (upargs.total_weight == NULL || upargs.total_minus_state == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1639:16: note: Assuming the condition is false
            || upargs.result_tmp == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1638:9: note: Taking false branch
        if (upargs.total_weight == NULL || upargs.total_minus_state == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1645:21: note: Assuming the condition is true
        for (j = 0; j < self->num_samples; j++) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1645:9: note: Loop condition is true.  Entering loop body
        for (j = 0; j < self->num_samples; j++) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1647:13: note: Loop condition is true.  Entering loop body
            for (k = 0; k < state_dim; k++) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1648:40: note: Assigned value is garbage or undefined
                upargs.total_weight[k] += weight_u[k];
                                       ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1677:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_site = !!(options & TSK_STAT_SITE);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1677:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_site = !!(options & TSK_STAT_SITE);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:49:38: note: expanded from macro 'TSK_STAT_SITE'
#define TSK_STAT_SITE               (1 << 0)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1678:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1678:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:50:38: note: expanded from macro 'TSK_STAT_BRANCH'
#define TSK_STAT_BRANCH             (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1679:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_node = !!(options & TSK_STAT_NODE);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1679:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_node = !!(options & TSK_STAT_NODE);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:51:38: note: expanded from macro 'TSK_STAT_NODE'
#define TSK_STAT_NODE               (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1719:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_SPAN_NORMALISE) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1719:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_SPAN_NORMALISE) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:55:38: note: expanded from macro 'TSK_STAT_SPAN_NORMALISE'
#define TSK_STAT_SPAN_NORMALISE     (1 << 11)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1732:78: warning: pointer parameter 'set_indexes' can be pointer to const [readability-non-const-parameter]
check_set_indexes(tsk_size_t num_sets, tsk_size_t num_set_indexes, tsk_id_t *set_indexes)
                                                                   ~~~~~~~~  ^
                                                                   const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1749:17: warning: pointer parameter 'sample_set_sizes' can be pointer to const [readability-non-const-parameter]
    tsk_size_t *sample_set_sizes, tsk_id_t *sample_sets)
    ~~~~~~~~~~  ^
    const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1749:45: warning: pointer parameter 'sample_sets' can be pointer to const [readability-non-const-parameter]
    tsk_size_t *sample_set_sizes, tsk_id_t *sample_sets)
                                  ~~~~~~~~  ^
                                  const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1804:15: warning: pointer parameter 'set_indexes' can be pointer to const [readability-non-const-parameter]
    tsk_id_t *set_indexes, general_stat_func_t *f, tsk_size_t num_windows,
    ~~~~~~~~  ^
    const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:1891:30: warning: Call to 'malloc' has an allocation size of 0 bytes [clang-analyzer-unix.API]
    tsk_size_t *coordinate = malloc(num_sample_sets * sizeof(*coordinate));
                             ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2201:23: note: Assuming the condition is false
    bool stat_site = !!(options & TSK_STAT_SITE);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2202:25: note: Assuming the condition is true
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2203:23: note: Assuming the condition is true
    bool stat_node = !!(options & TSK_STAT_NODE);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2215:5: note: Taking false branch
    if (stat_node) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2220:21: note: Left side of '||' is true
    if (!(stat_site || stat_branch)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2220:5: note: Taking false branch
    if (!(stat_site || stat_branch)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2224:5: note: Taking false branch
    if (stat_site + stat_branch > 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2228:9: note: Assuming 'windows' is not equal to NULL
    if (windows == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2228:5: note: Taking false branch
    if (windows == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2233:13: note: Assuming 'ret' is equal to 0
        if (ret != 0) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2233:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2239:9: note: Assuming 'ret' is equal to 0
    if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2239:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2246:9: note: Assuming 'counts' is not equal to NULL
    if (counts == NULL || result_dims == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2246:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:2246:27: note: Assuming 'result_dims' is not equal to NULL
    if (counts == NULL || result_dims == NULL) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2246:5: note: Taking false branch
    if (counts == NULL || result_dims == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2252:17: note: Assuming 'k' is >= 'num_sample_sets'
    for (k = 0; k < num_sample_sets; k++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2252:5: note: Loop condition is false. Execution continues on line 2266
    for (k = 0; k < num_sample_sets; k++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2266:17: note: Assuming the condition is false
    for (j = 0; j < self->num_samples; j++) {
                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2266:5: note: Loop condition is false. Execution continues on line 2271
    for (j = 0; j < self->num_samples; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2274:5: note: Taking true branch
    if (stat_site) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2275:15: note: Calling 'tsk_treeseq_site_allele_frequency_spectrum'
        ret = tsk_treeseq_site_allele_frequency_spectrum(self, num_sample_sets,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1956:9: note: Assuming 'parent' is not equal to NULL
    if (parent == NULL || total_counts == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1956:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:1956:27: note: Assuming 'total_counts' is not equal to NULL
    if (parent == NULL || total_counts == NULL) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1956:5: note: Taking false branch
    if (parent == NULL || total_counts == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1962:5: note: Loop condition is false. Execution continues on line 1965
    for (j = 0; j < num_sample_sets; j++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1973:12: note: Assuming 'tj' is >= 'num_edges'
    while (tj < num_edges || t_left < sequence_length) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1973:12: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:1973:5: note: Loop condition is true.  Entering loop body
    while (tj < num_edges || t_left < sequence_length) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1974:31: note: Left side of '&&' is false
        while (tk < num_edges && edge_right[O[tk]] == t_left) {
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1986:31: note: Left side of '&&' is false
        while (tj < num_edges && edge_left[I[tj]] == t_left) {
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1998:9: note: Taking false branch
        if (tj < num_edges) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2001:9: note: Taking false branch
        if (tk < num_edges) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2006:29: note: Assuming the condition is true
        for (tree_site = 0; tree_site < self->tree_sites_length[tree_index];
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2006:9: note: Loop condition is true.  Entering loop body
        for (tree_site = 0; tree_site < self->tree_sites_length[tree_index];
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2009:13: note: Loop condition is false. Execution continues on line 2013
            while (windows[window_index + 1] <= site->position) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2013:19: note: Calling 'tsk_treeseq_update_site_afs'
            ret = tsk_treeseq_update_site_afs(self, site, total_counts, counts,
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1891:30: note: Call to 'malloc' has an allocation size of 0 bytes
    tsk_size_t *coordinate = malloc(num_sample_sets * sizeof(*coordinate));
                             ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1892:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = !!(options & TSK_STAT_POLARISED);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1892:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = !!(options & TSK_STAT_POLARISED);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:54:38: note: expanded from macro 'TSK_STAT_POLARISED'
#define TSK_STAT_POLARISED          (1 << 10)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:1933:37: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    tsk_size_t num_windows, double *windows, tsk_size_t *result_dims, double *result,
                            ~~~~~~  ^
                            const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2044:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = !!(options & TSK_STAT_POLARISED);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2044:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool polarised = !!(options & TSK_STAT_POLARISED);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:54:38: note: expanded from macro 'TSK_STAT_POLARISED'
#define TSK_STAT_POLARISED          (1 << 10)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2076:81: warning: pointer parameter 'windows' can be pointer to const [readability-non-const-parameter]
    tsk_size_t num_sample_sets, double *counts, tsk_size_t num_windows, double *windows,
                                                                        ~~~~~~  ^
                                                                        const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2201:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_site = !!(options & TSK_STAT_SITE);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2201:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_site = !!(options & TSK_STAT_SITE);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:49:38: note: expanded from macro 'TSK_STAT_SITE'
#define TSK_STAT_SITE               (1 << 0)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2202:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2202:37: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_branch = !!(options & TSK_STAT_BRANCH);
                                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:50:38: note: expanded from macro 'TSK_STAT_BRANCH'
#define TSK_STAT_BRANCH             (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2203:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_node = !!(options & TSK_STAT_NODE);
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2203:35: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    bool stat_node = !!(options & TSK_STAT_NODE);
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:51:38: note: expanded from macro 'TSK_STAT_NODE'
#define TSK_STAT_NODE               (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2283:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_SPAN_NORMALISE) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2283:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_STAT_SPAN_NORMALISE) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:55:38: note: expanded from macro 'TSK_STAT_SPAN_NORMALISE'
#define TSK_STAT_SPAN_NORMALISE     (1 << 11)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:2297:50: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
diversity_summary_func(size_t state_dim, double *state, size_t TSK_UNUSED(result_dim),
                                         ~~~~~~  ^
                                         const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2323:57: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
trait_covariance_summary_func(size_t state_dim, double *state,
                                                ~~~~~~  ^
                                                const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2383:58: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
trait_correlation_summary_func(size_t state_dim, double *state,
                                                 ~~~~~~  ^
                                                 const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2465:31: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
    size_t state_dim, double *state, size_t result_dim, double *result, void *params)
                      ~~~~~~  ^
                      const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2577:58: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
segregating_sites_summary_func(size_t state_dim, double *state,
                                                 ~~~~~~  ^
                                                 const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2604:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
Y1_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2659:63: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
divergence_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                                      ~~~~~~  ^
                                                      const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2698:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
Y2_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2737:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
f2_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2782:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
Y3_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2824:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
f3_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:2871:55: warning: pointer parameter 'state' can be pointer to const [readability-non-const-parameter]
f4_summary_func(size_t TSK_UNUSED(state_dim), double *state, size_t result_dim,
                                              ~~~~~~  ^
                                              const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:3003:45: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    ret = tsk_treeseq_init(output, &tables, TSK_BUILD_INDEXES);
                                            ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:648:28: note: expanded from macro 'TSK_BUILD_INDEXES'
#define TSK_BUILD_INDEXES (1 << 0)
                           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3021:34: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const bool sample_counts = !(self->options & TSK_NO_SAMPLE_COUNTS);
                                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3021:50: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const bool sample_counts = !(self->options & TSK_NO_SAMPLE_COUNTS);
                                                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3022:34: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const bool sample_lists = !!(self->options & TSK_SAMPLE_LISTS);
                                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3022:50: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    const bool sample_lists = !!(self->options & TSK_SAMPLE_LISTS);
                                                 ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:9: warning: Potential memory leak [clang-analyzer-unix.Malloc]
    if (options & TSK_SAMPLE_COUNTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3124:37: note: Memory is allocated
        self->num_tracked_samples = calloc(num_nodes, sizeof(tsk_id_t));
                                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:42: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3136:16: note: Assuming the condition is false
            || self->next_sample == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:9: note: Taking false branch
        if (self->left_sample == NULL || self->right_sample == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Returned allocated memory
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:9: note: Potential memory leak
    if (options & TSK_SAMPLE_COUNTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_SAMPLE_COUNTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:19: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (options & TSK_SAMPLE_COUNTS) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:45:38: note: expanded from macro 'TSK_SAMPLE_COUNTS'
#define TSK_SAMPLE_COUNTS           (1 << 0)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3134:29: warning: Call to 'malloc' has an allocation size of 0 bytes [clang-analyzer-unix.API]
        self->next_sample = malloc(num_samples * sizeof(*self->next_sample));
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3134:29: note: Call to 'malloc' has an allocation size of 0 bytes
        self->next_sample = malloc(num_samples * sizeof(*self->next_sample));
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3193:15: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !!(self->options & TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3193:31: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !!(self->options & TSK_SAMPLE_LISTS);
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3199:14: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !(self->options & TSK_NO_SAMPLE_COUNTS);
             ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3199:30: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return !(self->options & TSK_NO_SAMPLE_COUNTS);
                             ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3218:61: warning: pointer parameter 'tracked_samples' can be pointer to const [readability-non-const-parameter]
    tsk_tree_t *self, size_t num_tracked_samples, tsk_id_t *tracked_samples)
                                                  ~~~~~~~~  ^
                                                  const 
/home/benj/projects/tskit/c/build/../tskit/trees.c:3303:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(options & TSK_NO_INIT)) {
                    ^
/home/benj/projects/tskit/c/build/../tskit/tables.h:622:22: note: expanded from macro 'TSK_NO_INIT'
#define TSK_NO_INIT (1u << 30)
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3329:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(dest->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3329:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(dest->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3330:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (self->options & TSK_NO_SAMPLE_COUNTS) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3330:29: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (self->options & TSK_NO_SAMPLE_COUNTS) {
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3339:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (dest->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3339:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (dest->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3340:15: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (!(self->options & TSK_SAMPLE_LISTS)) {
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3340:31: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (!(self->options & TSK_SAMPLE_LISTS)) {
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3478:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3478:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3497:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_NO_SAMPLE_COUNTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3497:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_NO_SAMPLE_COUNTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3669:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3669:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3681:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3681:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3709:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3709:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3718:13: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (self->options & TSK_SAMPLE_LISTS) {
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3718:29: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (self->options & TSK_SAMPLE_LISTS) {
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3721:15: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3721:31: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                              ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3808:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3808:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3852:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3852:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:11: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
          ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:27: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
                          ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:47:38: note: expanded from macro 'TSK_NO_SAMPLE_COUNTS'
#define TSK_NO_SAMPLE_COUNTS        (1 << 2)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:9: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:25: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    if (self->options & TSK_SAMPLE_LISTS) {
                        ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: warning: Potential leak of memory pointed to by 'left_child' [clang-analyzer-unix.Malloc]
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3107:24: note: Memory is allocated
    self->left_child = malloc(num_nodes * sizeof(tsk_id_t));
                       ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:42: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3136:16: note: Assuming the condition is false
            || self->next_sample == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:9: note: Taking false branch
        if (self->left_sample == NULL || self->right_sample == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Returned allocated memory
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is false. Execution continues on line 4935
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4939:5: note: Taking false branch
    if (ret != 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4943:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4950:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4953:19: note: Calling 'tsk_tree_next'
    while ((ret = tsk_tree_next(&trees[1])) == 1) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4122:5: note: Taking true branch
    if (self->index == -1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4123:15: note: Calling 'tsk_tree_first'
        ret = tsk_tree_first(self);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:9: note: Assuming the condition is true
    if (tables->edges.num_rows > 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:5: note: Taking true branch
    if (tables->edges.num_rows > 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4060:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4069:15: note: Calling 'tsk_tree_advance'
        ret = tsk_tree_advance(self, TSK_DIR_FORWARD, tables->edges.right,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3978:5: note: Taking true branch
    if (direction == TSK_DIR_FORWARD) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:5: note: Loop condition is false. Execution continues on line 3993
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:5: note: Loop condition is true.  Entering loop body
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3996:15: note: Calling 'tsk_tree_insert_edge'
        ret = tsk_tree_insert_edge(self, edge_parent[k], edge_child[k]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3878:5: note: Taking false branch
    if (parent[c] != TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:9: note: Assuming the condition is false
    if (u == TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:5: note: Taking false branch
    if (u == TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:16: note: Assuming the condition is false
        while (u != TSK_NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:9: note: Loop condition is false. Execution continues on line 3913
        while (u != TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3913:9: note: Taking false branch
        if (IS_ROOT(c)) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3938:35: note: Left side of '&&' is false
            if (IS_ROOT(path_end) && !path_end_was_root) {
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: note: Potential leak of memory pointed to by 'left_child'
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: warning: Potential leak of memory pointed to by 'parent' [clang-analyzer-unix.Malloc]
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3106:20: note: Memory is allocated
    self->parent = malloc(num_nodes * sizeof(tsk_id_t));
                   ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:42: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3136:16: note: Assuming the condition is false
            || self->next_sample == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:9: note: Taking false branch
        if (self->left_sample == NULL || self->right_sample == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Returned allocated memory
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is false. Execution continues on line 4935
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4939:5: note: Taking false branch
    if (ret != 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4943:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4950:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4953:19: note: Calling 'tsk_tree_next'
    while ((ret = tsk_tree_next(&trees[1])) == 1) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4122:5: note: Taking true branch
    if (self->index == -1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4123:15: note: Calling 'tsk_tree_first'
        ret = tsk_tree_first(self);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:9: note: Assuming the condition is true
    if (tables->edges.num_rows > 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:5: note: Taking true branch
    if (tables->edges.num_rows > 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4060:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4069:15: note: Calling 'tsk_tree_advance'
        ret = tsk_tree_advance(self, TSK_DIR_FORWARD, tables->edges.right,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3978:5: note: Taking true branch
    if (direction == TSK_DIR_FORWARD) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:5: note: Loop condition is false. Execution continues on line 3993
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:5: note: Loop condition is true.  Entering loop body
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3996:15: note: Calling 'tsk_tree_insert_edge'
        ret = tsk_tree_insert_edge(self, edge_parent[k], edge_child[k]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3878:5: note: Taking false branch
    if (parent[c] != TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:9: note: Assuming the condition is false
    if (u == TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:5: note: Taking false branch
    if (u == TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:16: note: Assuming the condition is false
        while (u != TSK_NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:9: note: Loop condition is false. Execution continues on line 3913
        while (u != TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3913:9: note: Taking false branch
        if (IS_ROOT(c)) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3938:35: note: Left side of '&&' is false
            if (IS_ROOT(path_end) && !path_end_was_root) {
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: note: Potential leak of memory pointed to by 'parent'
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: warning: Potential leak of memory pointed to by 'right_sib' [clang-analyzer-unix.Malloc]
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Calling 'tsk_tree_init'
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3090:5: note: Taking false branch
    if (tree_sequence == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3094:5: note: Taking false branch
    if (options & TSK_SAMPLE_COUNTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3110:23: note: Memory is allocated
    self->right_sib = malloc(num_nodes * sizeof(tsk_id_t));
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:33: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:61: note: Assuming the condition is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
                                                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:12: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:9: note: Left side of '||' is false
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3112:38: note: Assuming the condition is false
        || self->left_sib == NULL || self->right_sib == NULL) {
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3111:5: note: Taking false branch
    if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:9: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:33: note: Assuming the condition is false
    if (self->stack1 == NULL || self->stack2 == NULL) {
                                ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3119:5: note: Taking false branch
    if (self->stack1 == NULL || self->stack2 == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3122:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:42: note: Assuming the condition is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:13: note: Left side of '||' is false
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3127:16: note: Assuming the condition is false
            || self->marked == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3126:9: note: Taking false branch
        if (self->num_samples == NULL || self->num_tracked_samples == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3131:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:42: note: Assuming the condition is false
        if (self->left_sample == NULL || self->right_sample == NULL
                                         ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:13: note: Left side of '||' is false
        if (self->left_sample == NULL || self->right_sample == NULL
            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3136:16: note: Assuming the condition is false
            || self->next_sample == NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3135:9: note: Taking false branch
        if (self->left_sample == NULL || self->right_sample == NULL
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:15: note: Returned allocated memory
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is false. Execution continues on line 4935
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4939:5: note: Taking false branch
    if (ret != 1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4943:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4950:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4953:19: note: Calling 'tsk_tree_next'
    while ((ret = tsk_tree_next(&trees[1])) == 1) {
                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4122:5: note: Taking true branch
    if (self->index == -1) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4123:15: note: Calling 'tsk_tree_first'
        ret = tsk_tree_first(self);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:9: note: Assuming the condition is true
    if (tables->edges.num_rows > 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4054:5: note: Taking true branch
    if (tables->edges.num_rows > 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4060:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4069:15: note: Calling 'tsk_tree_advance'
        ret = tsk_tree_advance(self, TSK_DIR_FORWARD, tables->edges.right,
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3978:5: note: Taking true branch
    if (direction == TSK_DIR_FORWARD) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3983:5: note: Loop condition is false. Execution continues on line 3993
    while (out >= 0 && out < num_edges && out_breakpoints[out_order[out]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:12: note: Left side of '&&' is true
/home/benj/projects/tskit/c/build/../tskit/trees.c:3993:5: note: Loop condition is true.  Entering loop body
    while (in >= 0 && in < num_edges && in_breakpoints[in_order[in]] == x) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3996:15: note: Calling 'tsk_tree_insert_edge'
        ret = tsk_tree_insert_edge(self, edge_parent[k], edge_child[k]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3878:5: note: Taking false branch
    if (parent[c] != TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:9: note: Assuming the condition is false
    if (u == TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3886:5: note: Taking false branch
    if (u == TSK_NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3897:5: note: Taking true branch
    if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:16: note: Assuming the condition is false
        while (u != TSK_NULL) {
               ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3904:9: note: Loop condition is false. Execution continues on line 3913
        while (u != TSK_NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3913:9: note: Taking false branch
        if (IS_ROOT(c)) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3938:35: note: Left side of '&&' is false
            if (IS_ROOT(path_end) && !path_end_was_root) {
                                  ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3953:5: note: Taking true branch
    if (self->options & TSK_SAMPLE_LISTS) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:3957:12: note: Potential leak of memory pointed to by 'right_sib'
    return ret;
           ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4157:21: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return value | (1ULL << bit);
                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4163:22: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
    return (value & (1ULL << bit)) != 0;
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4348:23: warning: Potential memory leak [clang-analyzer-unix.Malloc]
    self->num_nodes = tsk_treeseq_get_num_nodes(tree_sequence);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is true.  Entering loop body
/home/benj/projects/tskit/c/build/../tskit/trees.c:4906:5: note: Loop condition is false. Execution continues on line 4914
/home/benj/projects/tskit/c/build/../tskit/trees.c:4915:5: note: Taking false branch
    if (ret != 0) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4925:15: note: Calling 'tsk_diff_iter_init'
        ret = tsk_diff_iter_init(&diff_iters[i], treeseqs[i]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4355:29: note: Memory is allocated
    self->edge_list_nodes = malloc(self->num_edges * sizeof(*self->edge_list_nodes));
                            ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4356:9: note: Assuming the condition is false
    if (self->edge_list_nodes == NULL) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4356:5: note: Taking false branch
    if (self->edge_list_nodes == NULL) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4925:15: note: Returned allocated memory
        ret = tsk_diff_iter_init(&diff_iters[i], treeseqs[i]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4926:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4930:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4920:5: note: Loop condition is true.  Entering loop body
    for (i = 0; i < 2; i++) {
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4922:9: note: Taking false branch
        if (ret != 0) {
        ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4925:15: note: Calling 'tsk_diff_iter_init'
        ret = tsk_diff_iter_init(&diff_iters[i], treeseqs[i]);
              ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4348:23: note: Potential memory leak
    self->num_nodes = tsk_treeseq_get_num_nodes(tree_sequence);
                      ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4506:22: warning: either cast from 'int' to 'size_t' (aka 'unsigned long') is ineffective, or there is loss of precision before the conversion [misc-misplaced-widening-cast]
    self->m = calloc((size_t)(self->N + self->n), sizeof(tsk_size_t));
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4507:22: warning: either cast from 'int' to 'size_t' (aka 'unsigned long') is ineffective, or there is loss of precision before the conversion [misc-misplaced-widening-cast]
    self->M = calloc((size_t)(self->N + self->n), sizeof(double));
                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4826:17: warning: redundant cast to the same type [google-readability-casting]
        depth = (tsk_size_t) stack[stack_top].depth;
                ^~~~~~~~~~~~~~~~~~
/home/benj/projects/tskit/c/build/../tskit/trees.c:4921:53: warning: use of a signed integer operand with a binary bitwise operator [hicpp-signed-bitwise]
        ret = tsk_tree_init(&trees[i], treeseqs[i], TSK_SAMPLE_LISTS);
                                                    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:46:38: note: expanded from macro 'TSK_SAMPLE_LISTS'
#define TSK_SAMPLE_LISTS            (1 << 1)
                                     ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:225:5: warning: function 'tsk_treeseq_load' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_treeseq_load(tsk_treeseq_t *self, const char *filename, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:437:1: note: the definition seen here
tsk_treeseq_load(
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:225:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_treeseq_load(tsk_treeseq_t *self, const char *filename, tsk_flags_t options);
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:275:5: warning: function 'tsk_treeseq_genealogical_nearest_neighbours' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_treeseq_genealogical_nearest_neighbours(tsk_treeseq_t *self, tsk_id_t *focal,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:604:1: note: the definition seen here
tsk_treeseq_genealogical_nearest_neighbours(tsk_treeseq_t *self, tsk_id_t *focal,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:275:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_treeseq_genealogical_nearest_neighbours(tsk_treeseq_t *self, tsk_id_t *focal,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:278:5: warning: function 'tsk_treeseq_mean_descendants' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_treeseq_mean_descendants(tsk_treeseq_t *self, tsk_id_t **reference_sets,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:786:1: note: the definition seen here
tsk_treeseq_mean_descendants(tsk_treeseq_t *self, tsk_id_t **reference_sets,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:278:5: note: differing parameters are named here: ('options'), in definition: ('TSK_UNUSED_options')
int tsk_treeseq_mean_descendants(tsk_treeseq_t *self, tsk_id_t **reference_sets,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:286:5: warning: function 'tsk_treeseq_general_stat' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_treeseq_general_stat(tsk_treeseq_t *self, size_t K, double *W, size_t M,
    ^                                                    ~~         ~~        ~~
                                                         state_dim  sample_weights result_dim
/home/benj/projects/tskit/c/build/../tskit/trees.c:1672:1: note: the definition seen here
tsk_treeseq_general_stat(tsk_treeseq_t *self, size_t state_dim, double *sample_weights,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:286:5: note: differing parameters are named here: ('K', 'W', 'M', 'sigma'), in definition: ('state_dim', 'sample_weights', 'result_dim', 'result')
int tsk_treeseq_general_stat(tsk_treeseq_t *self, size_t K, double *W, size_t M,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:393:5: warning: function 'tsk_tree_depth' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_tree_depth(tsk_tree_t *self, tsk_id_t u, tsk_size_t *depth);
    ^                                                        ~~~~~~
                                                             depth_ret
/home/benj/projects/tskit/c/build/../tskit/trees.c:3584:1: note: the definition seen here
tsk_tree_depth(tsk_tree_t *self, tsk_id_t u, tsk_size_t *depth_ret)
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:393:5: note: differing parameters are named here: ('depth'), in definition: ('depth_ret')
int tsk_tree_depth(tsk_tree_t *self, tsk_id_t u, tsk_size_t *depth);
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:401:5: warning: function 'tsk_tree_map_mutations' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_tree_map_mutations(tsk_tree_t *self, int8_t *genotypes, double *cost_matrix,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.c:4188:1: note: the definition seen here
tsk_tree_map_mutations(tsk_tree_t *self, int8_t *genotypes,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:401:5: note: differing parameters are named here: ('cost_matrix', 'options', 'ancestral_state', 'num_transitions', 'transitions'), in definition: ('TSK_UNUSED_cost_matrix', 'TSK_UNUSED_options', 'r_ancestral_state', 'r_num_transitions', 'r_transitions')
int tsk_tree_map_mutations(tsk_tree_t *self, int8_t *genotypes, double *cost_matrix,
    ^
/home/benj/projects/tskit/c/build/../tskit/trees.h:414:5: warning: function 'tsk_diff_iter_next' has a definition with different parameter names [readability-inconsistent-declaration-parameter-name]
int tsk_diff_iter_next(tsk_diff_iter_t *self, double *left, double *right,
    ^                                                 ~~~~~         ~~~~~~
                                                      ret_left      ret_right
/home/benj/projects/tskit/c/build/../tskit/trees.c:4383:1: note: the definition seen here
tsk_diff_iter_next(tsk_diff_iter_t *self, double *ret_left, double *ret_right,
^
/home/benj/projects/tskit/c/build/../tskit/trees.h:414:5: note: differing parameters are named here: ('left', 'right', 'edges_out', 'edges_in'), in definition: ('ret_left', 'ret_right', 'edges_out_ret', 'edges_in_ret')
int tsk_diff_iter_next(tsk_diff_iter_t *self, double *left, double *right,
    ^