VariantBam thread locks -- helgrind

helgrind-t0.txt

==16320== Helgrind, a thread error detector
==16320== Copyright (C) 2007-2015, and GNU GPL'd, by OpenWorks LLP et al.
==16320== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info
==16320== Command: variant Test1-sort.bam -b -t 0 -o /dev/null
==16320== 
--16320-- Valgrind options:
--16320--    -v
--16320--    --tool=helgrind
--16320-- Contents of /proc/version:
--16320--   Linux version 4.4.0-59-generic (buildd@lgw01-11) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) ) #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017
--16320-- 
--16320-- Arch and hwcaps: AMD64, LittleEndian, amd64-cx16-lzcnt-rdtscp-sse3-avx-avx2-bmi
--16320-- Page sizes: currently 4096, max supported 4096
--16320-- Valgrind library directory: /usr/lib/valgrind
--16320-- Reading syms from /mnt/work/bcbio/anaconda/bin/variant
--16320-- warning: DiCfSI 0x0 .. 0x1 outside mapped rx segments (NONE)
--16320-- warning: DiCfSI 0x2 .. 0x3 outside mapped rx segments (NONE)
--16320-- warning: DiCfSI 0x4 .. 0x4 outside mapped rx segments (NONE)
--16320-- warning: DiCfSI 0x5 .. 0x8 outside mapped rx segments (NONE)
--16320-- warning: DiCfSI 0x9 .. 0xc outside mapped rx segments (NONE)
--16320-- warning: DiCfSI 0xd .. 0x165 outside mapped rx segments (NONE)
--16320-- warning: DiCfSI 0x166 .. 0x166 outside mapped rx segments (NONE)
--16320-- warning: DiCfSI 0x167 .. 0x167 outside mapped rx segments (NONE)
--16320-- warning: DiCfSI 0x168 .. 0x169 outside mapped rx segments (NONE)
--16320-- warning: DiCfSI 0x16a .. 0x16b outside mapped rx segments (NONE)
==16320== Warning: DWARF2 reader: Badly formed extended line op encountered
==16320== Warning: DWARF2 reader: Badly formed extended line op encountered
[... snip a million of these messages ...]
==16320== Warning: DWARF2 reader: Badly formed extended line op encountered
--16320-- Reading syms from /lib/x86_64-linux-gnu/ld-2.23.so
--16320--   Considering /lib/x86_64-linux-gnu/ld-2.23.so ..
--16320--   .. CRC mismatch (computed 9bc477cd wanted 3da2f12a)
--16320--   Considering /usr/lib/debug/lib/x86_64-linux-gnu/ld-2.23.so ..
--16320--   .. CRC is valid
--16320-- Reading syms from /usr/lib/valgrind/helgrind-amd64-linux
--16320--   Considering /usr/lib/valgrind/helgrind-amd64-linux ..
--16320--   .. CRC mismatch (computed b2178fda wanted 9c894282)
--16320--    object doesn't have a symbol table
--16320--    object doesn't have a dynamic symbol table
--16320-- Scheduler: using generic scheduler lock implementation.
--16320-- Reading suppressions file: /usr/lib/valgrind/default.supp
==16320== embedded gdbserver: reading from /tmp/vgdb-pipe-from-vgdb-to-16320-by-ubuntu-on-???
==16320== embedded gdbserver: writing to   /tmp/vgdb-pipe-to-vgdb-from-16320-by-ubuntu-on-???
==16320== embedded gdbserver: shared mem   /tmp/vgdb-pipe-shared-mem-vgdb-16320-by-ubuntu-on-???
==16320== 
==16320== TO CONTROL THIS PROCESS USING vgdb (which you probably
==16320== don't want to do, unless you know exactly what you're doing,
==16320== or are doing some strange experiment):
==16320==   /usr/lib/valgrind/../../bin/vgdb --pid=16320 ...command...
==16320== 
==16320== TO DEBUG THIS PROCESS USING GDB: start GDB like this
==16320==   /path/to/gdb variant
==16320== and then give GDB the following command
==16320==   target remote | /usr/lib/valgrind/../../bin/vgdb --pid=16320
==16320== --pid is optional if only one valgrind process is running
==16320== 
--16320-- Reading syms from /usr/lib/valgrind/vgpreload_core-amd64-linux.so
--16320--   Considering /usr/lib/valgrind/vgpreload_core-amd64-linux.so ..
--16320--   .. CRC mismatch (computed 2567ccf6 wanted 49420590)
--16320--    object doesn't have a symbol table
--16320-- Reading syms from /usr/lib/valgrind/vgpreload_helgrind-amd64-linux.so
--16320--   Considering /usr/lib/valgrind/vgpreload_helgrind-amd64-linux.so ..
--16320--   .. CRC mismatch (computed 4fc8b0b2 wanted 80b49e71)
--16320--    object doesn't have a symbol table
--16320-- REDIR: 0x401b8e0 (ld-linux-x86-64.so.2:index) redirected to 0x4c36ef0 (index)
--16320-- REDIR: 0x401bb00 (ld-linux-x86-64.so.2:strcmp) redirected to 0x4c37e00 (strcmp)
--16320-- REDIR: 0x401cf90 (ld-linux-x86-64.so.2:strlen) redirected to 0x4c37150 (strlen)
--16320-- REDIR: 0x401dcf0 (ld-linux-x86-64.so.2:mempcpy) redirected to 0x4c3a3a0 (mempcpy)
--16320-- Reading syms from /lib/x86_64-linux-gnu/librt-2.23.so
--16320--   Considering /lib/x86_64-linux-gnu/librt-2.23.so ..
--16320--   .. CRC mismatch (computed 53afabad wanted 7e68d3a3)
--16320--   Considering /usr/lib/debug/lib/x86_64-linux-gnu/librt-2.23.so ..
--16320--   .. CRC is valid
--16320-- Reading syms from /mnt/work/bcbio/anaconda/lib/libz.so.1.2.8
--16320-- Reading syms from /mnt/work/bcbio/anaconda/lib/libbz2.so.1.0.6
--16320-- Reading syms from /mnt/work/bcbio/anaconda/lib/liblzma.so.5.2.2
--16320-- Reading syms from /lib/x86_64-linux-gnu/libpthread-2.23.so
--16320--   Considering /usr/lib/debug/.build-id/27/f189ef8db8c3734c6a678e6ef3cb0b206d58b2.debug ..
--16320--   .. build-id is valid
==16320== WARNING: new redirection conflicts with existing -- ignoring it
--16320--     old: 0x056a0eb0 (pthread_spin_init   ) W-> (0000.0) 0x04c365e0 pthread_spin_init
--16320--     new: 0x056a0eb0 (pthread_spin_init   ) W-> (0000.0) 0x04c365f0 pthread_spin_unlock
==16320== WARNING: new redirection conflicts with existing -- ignoring it
--16320--     old: 0x056a2940 (sem_wait@@GLIBC_2.2.) W-> (0000.0) 0x04c366d0 sem_wait@*
--16320--     new: 0x056a2940 (sem_wait@@GLIBC_2.2.) W-> (0000.0) 0x04c366c0 sem_wait
==16320== WARNING: new redirection conflicts with existing -- ignoring it
--16320--     old: 0x056a2bc0 (sem_post@@GLIBC_2.2.) W-> (0000.0) 0x04c366f0 sem_post@*
--16320--     new: 0x056a2bc0 (sem_post@@GLIBC_2.2.) W-> (0000.0) 0x04c366e0 sem_post
--16320-- Reading syms from /mnt/work/bcbio/anaconda/lib/libstdc++.so.6.0.21
--16320-- ELF section outside all mapped regions
--16320-- Reading syms from /mnt/work/bcbio/anaconda/lib/libstdc++.so.6.0.21
--16320--    object doesn't have a symbol table
--16320-- Reading syms from /lib/x86_64-linux-gnu/libm-2.23.so
--16320--   Considering /lib/x86_64-linux-gnu/libm-2.23.so ..
--16320--   .. CRC mismatch (computed 8bd88005 wanted 32b88176)
--16320--   Considering /usr/lib/debug/lib/x86_64-linux-gnu/libm-2.23.so ..
--16320--   .. CRC is valid
--16320-- Reading syms from /mnt/work/bcbio/anaconda/lib/libgcc_s.so.1
--16320-- ELF section outside all mapped regions
--16320-- Reading syms from /mnt/work/bcbio/anaconda/lib/libgcc_s.so.1
--16320-- Reading syms from /lib/x86_64-linux-gnu/libc-2.23.so
--16320--   Considering /lib/x86_64-linux-gnu/libc-2.23.so ..
--16320--   .. CRC mismatch (computed b2979fac wanted 1affc958)
--16320--   Considering /usr/lib/debug/lib/x86_64-linux-gnu/libc-2.23.so ..
--16320--   .. CRC is valid
--16320-- REDIR: 0x621ba00 (libc.so.6:strcasecmp) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x6217280 (libc.so.6:strcspn) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x621dcf0 (libc.so.6:strncasecmp) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x62196f0 (libc.so.6:strpbrk) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x6219a80 (libc.so.6:strspn) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x621b14b (libc.so.6:memcpy@GLIBC_2.2.5) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x6219400 (libc.so.6:rindex) redirected to 0x4c36bd0 (rindex)
--16320-- REDIR: 0x6210130 (libc.so.6:malloc) redirected to 0x4c2ef40 (malloc)
--16320-- REDIR: 0x6217720 (libc.so.6:strlen) redirected to 0x4c37090 (strlen)
--16320-- REDIR: 0x621abf0 (libc.so.6:__GI_memcmp) redirected to 0x4c39380 (__GI_memcmp)
--16320-- REDIR: 0x6215cd0 (libc.so.6:strcmp) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x622b570 (libc.so.6:__strcmp_sse2_unaligned) redirected to 0x4c37cc0 (strcmp)
--16320-- REDIR: 0x593dbd0 (libstdc++.so.6:operator new(unsigned long)) redirected to 0x4c2f4a0 (operator new(unsigned long))
--16320-- REDIR: 0x62d9970 (libc.so.6:__memmove_avx_unaligned) redirected to 0x4c37f60 (memcpy@GLIBC_2.2.5)
--16320-- REDIR: 0x6210d10 (libc.so.6:calloc) redirected to 0x4c30ec0 (calloc)
--16320-- REDIR: 0x6215ab0 (libc.so.6:__GI_strchr) redirected to 0x4c36d30 (__GI_strchr)
--16320-- REDIR: 0x593bde0 (libstdc++.so.6:operator delete(void*)) redirected to 0x4c30600 (operator delete(void*))
--16320-- REDIR: 0x621abb0 (libc.so.6:bcmp) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x62fa3f0 (libc.so.6:__memcmp_sse4_1) redirected to 0x4c394c0 (__memcmp_sse4_1)
--16320-- REDIR: 0x621b1b0 (libc.so.6:memset) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x62fe930 (libc.so.6:__memset_avx2) redirected to 0x4c39830 (memset)
--16320-- REDIR: 0x62193c0 (libc.so.6:strncpy) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x6232000 (libc.so.6:__strncpy_sse2_unaligned) redirected to 0x4c37350 (__strncpy_sse2_unaligned)
--16320-- REDIR: 0x6215a80 (libc.so.6:index) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16320-- REDIR: 0x6220470 (libc.so.6:__GI_memcpy) redirected to 0x4c386b0 (__GI_memcpy)
--16320-- REDIR: 0x62104f0 (libc.so.6:free) redirected to 0x4c301a0 (free)
--16320-- REDIR: 0x62106c0 (libc.so.6:realloc) redirected to 0x4c31100 (realloc)
--16320-- REDIR: 0x569cd40 (libpthread.so.0:pthread_mutex_lock) redirected to 0x4c360e0 (pthread_mutex_lock)
--16320-- REDIR: 0x569e4c0 (libpthread.so.0:pthread_mutex_unlock) redirected to 0x4c36110 (pthread_mutex_unlock)
==16320== 
==16320== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==16320== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

helgrind-t2-lock.txt

==16284== Helgrind, a thread error detector
==16284== Copyright (C) 2007-2015, and GNU GPL'd, by OpenWorks LLP et al.
==16284== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info
==16284== Command: /mnt/work/bcbio/anaconda/bin/variant Test1-sort.bam -b -t 2 -o /dev/null
==16284== 
--16284-- Valgrind options:
--16284--    -v
--16284--    --tool=helgrind
--16284-- Contents of /proc/version:
--16284--   Linux version 4.4.0-59-generic (buildd@lgw01-11) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) ) #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017
--16284-- 
--16284-- Arch and hwcaps: AMD64, LittleEndian, amd64-cx16-lzcnt-rdtscp-sse3-avx-avx2-bmi
--16284-- Page sizes: currently 4096, max supported 4096
--16284-- Valgrind library directory: /usr/lib/valgrind
--16284-- Reading syms from /mnt/work/bcbio/anaconda/bin/variant
--16284-- warning: DiCfSI 0x0 .. 0x1 outside mapped rx segments (NONE)
--16284-- warning: DiCfSI 0x2 .. 0x3 outside mapped rx segments (NONE)
--16284-- warning: DiCfSI 0x4 .. 0x4 outside mapped rx segments (NONE)
--16284-- warning: DiCfSI 0x5 .. 0x8 outside mapped rx segments (NONE)
--16284-- warning: DiCfSI 0x9 .. 0xc outside mapped rx segments (NONE)
--16284-- warning: DiCfSI 0xd .. 0x165 outside mapped rx segments (NONE)
--16284-- warning: DiCfSI 0x166 .. 0x166 outside mapped rx segments (NONE)
--16284-- warning: DiCfSI 0x167 .. 0x167 outside mapped rx segments (NONE)
--16284-- warning: DiCfSI 0x168 .. 0x169 outside mapped rx segments (NONE)
--16284-- warning: DiCfSI 0x16a .. 0x16b outside mapped rx segments (NONE)
==16284== Warning: DWARF2 reader: Badly formed extended line op encountered
==16284== Warning: DWARF2 reader: Badly formed extended line op encountered
[... snip a million of these messages ...]
==16284== Warning: DWARF2 reader: Badly formed extended line op encountered
--16284-- Reading syms from /lib/x86_64-linux-gnu/ld-2.23.so
--16284--   Considering /lib/x86_64-linux-gnu/ld-2.23.so ..
--16284--   .. CRC mismatch (computed 9bc477cd wanted 3da2f12a)
--16284--   Considering /usr/lib/debug/lib/x86_64-linux-gnu/ld-2.23.so ..
--16284--   .. CRC is valid
--16284-- Reading syms from /usr/lib/valgrind/helgrind-amd64-linux
--16284--   Considering /usr/lib/valgrind/helgrind-amd64-linux ..
--16284--   .. CRC mismatch (computed b2178fda wanted 9c894282)
--16284--    object doesn't have a symbol table
--16284--    object doesn't have a dynamic symbol table
--16284-- Scheduler: using generic scheduler lock implementation.
--16284-- Reading suppressions file: /usr/lib/valgrind/default.supp
==16284== embedded gdbserver: reading from /tmp/vgdb-pipe-from-vgdb-to-16284-by-ubuntu-on-???
==16284== embedded gdbserver: writing to   /tmp/vgdb-pipe-to-vgdb-from-16284-by-ubuntu-on-???
==16284== embedded gdbserver: shared mem   /tmp/vgdb-pipe-shared-mem-vgdb-16284-by-ubuntu-on-???
==16284== 
==16284== TO CONTROL THIS PROCESS USING vgdb (which you probably
==16284== don't want to do, unless you know exactly what you're doing,
==16284== or are doing some strange experiment):
==16284==   /usr/lib/valgrind/../../bin/vgdb --pid=16284 ...command...
==16284== 
==16284== TO DEBUG THIS PROCESS USING GDB: start GDB like this
==16284==   /path/to/gdb /mnt/work/bcbio/anaconda/bin/variant
==16284== and then give GDB the following command
==16284==   target remote | /usr/lib/valgrind/../../bin/vgdb --pid=16284
==16284== --pid is optional if only one valgrind process is running
==16284== 
--16284-- Reading syms from /usr/lib/valgrind/vgpreload_core-amd64-linux.so
--16284--   Considering /usr/lib/valgrind/vgpreload_core-amd64-linux.so ..
--16284--   .. CRC mismatch (computed 2567ccf6 wanted 49420590)
--16284--    object doesn't have a symbol table
--16284-- Reading syms from /usr/lib/valgrind/vgpreload_helgrind-amd64-linux.so
--16284--   Considering /usr/lib/valgrind/vgpreload_helgrind-amd64-linux.so ..
--16284--   .. CRC mismatch (computed 4fc8b0b2 wanted 80b49e71)
--16284--    object doesn't have a symbol table
--16284-- REDIR: 0x401b8e0 (ld-linux-x86-64.so.2:index) redirected to 0x4c36ef0 (index)
--16284-- REDIR: 0x401bb00 (ld-linux-x86-64.so.2:strcmp) redirected to 0x4c37e00 (strcmp)
--16284-- REDIR: 0x401cf90 (ld-linux-x86-64.so.2:strlen) redirected to 0x4c37150 (strlen)
--16284-- REDIR: 0x401dcf0 (ld-linux-x86-64.so.2:mempcpy) redirected to 0x4c3a3a0 (mempcpy)
--16284-- Reading syms from /lib/x86_64-linux-gnu/librt-2.23.so
--16284--   Considering /lib/x86_64-linux-gnu/librt-2.23.so ..
--16284--   .. CRC mismatch (computed 53afabad wanted 7e68d3a3)
--16284--   Considering /usr/lib/debug/lib/x86_64-linux-gnu/librt-2.23.so ..
--16284--   .. CRC is valid
--16284-- Reading syms from /mnt/work/bcbio/anaconda/lib/libz.so.1.2.8
--16284-- Reading syms from /mnt/work/bcbio/anaconda/lib/libbz2.so.1.0.6
--16284-- Reading syms from /mnt/work/bcbio/anaconda/lib/liblzma.so.5.2.2
--16284-- Reading syms from /lib/x86_64-linux-gnu/libpthread-2.23.so
--16284--   Considering /usr/lib/debug/.build-id/27/f189ef8db8c3734c6a678e6ef3cb0b206d58b2.debug ..
--16284--   .. build-id is valid
==16284== WARNING: new redirection conflicts with existing -- ignoring it
--16284--     old: 0x056a0eb0 (pthread_spin_init   ) W-> (0000.0) 0x04c365e0 pthread_spin_init
--16284--     new: 0x056a0eb0 (pthread_spin_init   ) W-> (0000.0) 0x04c365f0 pthread_spin_unlock
==16284== WARNING: new redirection conflicts with existing -- ignoring it
--16284--     old: 0x056a2940 (sem_wait@@GLIBC_2.2.) W-> (0000.0) 0x04c366d0 sem_wait@*
--16284--     new: 0x056a2940 (sem_wait@@GLIBC_2.2.) W-> (0000.0) 0x04c366c0 sem_wait
==16284== WARNING: new redirection conflicts with existing -- ignoring it
--16284--     old: 0x056a2bc0 (sem_post@@GLIBC_2.2.) W-> (0000.0) 0x04c366f0 sem_post@*
--16284--     new: 0x056a2bc0 (sem_post@@GLIBC_2.2.) W-> (0000.0) 0x04c366e0 sem_post
--16284-- Reading syms from /mnt/work/bcbio/anaconda/lib/libstdc++.so.6.0.21
--16284-- ELF section outside all mapped regions
--16284-- Reading syms from /mnt/work/bcbio/anaconda/lib/libstdc++.so.6.0.21
--16284--    object doesn't have a symbol table
--16284-- Reading syms from /lib/x86_64-linux-gnu/libm-2.23.so
--16284--   Considering /lib/x86_64-linux-gnu/libm-2.23.so ..
--16284--   .. CRC mismatch (computed 8bd88005 wanted 32b88176)
--16284--   Considering /usr/lib/debug/lib/x86_64-linux-gnu/libm-2.23.so ..
--16284--   .. CRC is valid
--16284-- Reading syms from /mnt/work/bcbio/anaconda/lib/libgcc_s.so.1
--16284-- ELF section outside all mapped regions
--16284-- Reading syms from /mnt/work/bcbio/anaconda/lib/libgcc_s.so.1
--16284-- Reading syms from /lib/x86_64-linux-gnu/libc-2.23.so
--16284--   Considering /lib/x86_64-linux-gnu/libc-2.23.so ..
--16284--   .. CRC mismatch (computed b2979fac wanted 1affc958)
--16284--   Considering /usr/lib/debug/lib/x86_64-linux-gnu/libc-2.23.so ..
--16284--   .. CRC is valid
--16284-- REDIR: 0x621ba00 (libc.so.6:strcasecmp) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x6217280 (libc.so.6:strcspn) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x621dcf0 (libc.so.6:strncasecmp) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x62196f0 (libc.so.6:strpbrk) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x6219a80 (libc.so.6:strspn) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x621b14b (libc.so.6:memcpy@GLIBC_2.2.5) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x6219400 (libc.so.6:rindex) redirected to 0x4c36bd0 (rindex)
--16284-- REDIR: 0x6210130 (libc.so.6:malloc) redirected to 0x4c2ef40 (malloc)
--16284-- REDIR: 0x6217720 (libc.so.6:strlen) redirected to 0x4c37090 (strlen)
--16284-- REDIR: 0x621abf0 (libc.so.6:__GI_memcmp) redirected to 0x4c39380 (__GI_memcmp)
--16284-- REDIR: 0x6215cd0 (libc.so.6:strcmp) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x622b570 (libc.so.6:__strcmp_sse2_unaligned) redirected to 0x4c37cc0 (strcmp)
--16284-- REDIR: 0x593dbd0 (libstdc++.so.6:operator new(unsigned long)) redirected to 0x4c2f4a0 (operator new(unsigned long))
--16284-- REDIR: 0x62d9970 (libc.so.6:__memmove_avx_unaligned) redirected to 0x4c37f60 (memcpy@GLIBC_2.2.5)
--16284-- REDIR: 0x6210d10 (libc.so.6:calloc) redirected to 0x4c30ec0 (calloc)
--16284-- REDIR: 0x6215ab0 (libc.so.6:__GI_strchr) redirected to 0x4c36d30 (__GI_strchr)
--16284-- REDIR: 0x593bde0 (libstdc++.so.6:operator delete(void*)) redirected to 0x4c30600 (operator delete(void*))
--16284-- REDIR: 0x621abb0 (libc.so.6:bcmp) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x62fa3f0 (libc.so.6:__memcmp_sse4_1) redirected to 0x4c394c0 (__memcmp_sse4_1)
--16284-- REDIR: 0x621b1b0 (libc.so.6:memset) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x62fe930 (libc.so.6:__memset_avx2) redirected to 0x4c39830 (memset)
--16284-- REDIR: 0x569c5a0 (libpthread.so.0:pthread_mutex_init) redirected to 0x4c35f10 (pthread_mutex_init)
--16284-- REDIR: 0x569cd40 (libpthread.so.0:pthread_mutex_lock) redirected to 0x4c360e0 (pthread_mutex_lock)
--16284-- REDIR: 0x56a00c0 (libpthread.so.0:pthread_cond_init@@GLIBC_2.3.2) redirected to 0x4c36160 (pthread_cond_init@*)
--16284-- REDIR: 0x569a990 (libpthread.so.0:pthread_create@@GLIBC_2.2.5) redirected to 0x4c35cc0 (pthread_create@*)
--16284-- REDIR: 0x569e4c0 (libpthread.so.0:pthread_mutex_unlock) redirected to 0x4c36110 (pthread_mutex_unlock)
--16284-- REDIR: 0x62193c0 (libc.so.6:strncpy) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x6232000 (libc.so.6:__strncpy_sse2_unaligned) redirected to 0x4c37350 (__strncpy_sse2_unaligned)
--16284-- REDIR: 0x6215a80 (libc.so.6:index) redirected to 0x4a286f0 (_vgnU_ifunc_wrapper)
--16284-- REDIR: 0x6220470 (libc.so.6:__GI_memcpy) redirected to 0x4c386b0 (__GI_memcpy)
--16284-- REDIR: 0x62104f0 (libc.so.6:free) redirected to 0x4c301a0 (free)
--16284-- REDIR: 0x56a02a0 (libpthread.so.0:pthread_cond_wait@@GLIBC_2.3.2) redirected to 0x4c36120 (pthread_cond_wait@*)
--16284-- REDIR: 0x62106c0 (libc.so.6:realloc) redirected to 0x4c31100 (realloc)
--16284-- REDIR: 0x56a09c0 (libpthread.so.0:pthread_cond_signal@@GLIBC_2.3.2) redirected to 0x4c36140 (pthread_cond_signal@*)
--16284-- REDIR: 0x56a05e0 (libpthread.so.0:pthread_cond_timedwait@@GLIBC_2.3.2) redirected to 0x4c36130 (pthread_cond_timedwait@*)
==16284== 
==16284== Process terminating with default action of signal 2 (SIGINT)
==16284==    at 0x56A0709: pthread_cond_timedwait@@GLIBC_2.3.2 (pthread_cond_timedwait.S:225)
==16284==    by 0x4C35A19: ??? (in /usr/lib/valgrind/vgpreload_helgrind-amd64-linux.so)
==16284==    by 0x46CA7B: hts_tpool_next_result_wait (???:261)
==16284==    by 0x49E908: bgzf_read_block (in /mnt/work/bcbio/anaconda/bin/variant)
==16284==    by 0x49F9EE: bgzf_read (in /mnt/work/bcbio/anaconda/bin/variant)
==16284==    by 0x460523: bam_hdr_read (???:368)
==16284==    by 0x462C70: sam_hdr_read (???:1048)
==16284==    by 0x447D39: SeqLib::_Bam::open_BAM_for_reading(SeqLib::ThreadPool) (???:212)
==16284==    by 0x449BC9: SeqLib::BamReader::Open(std::string const&) (???:152)
==16284==    by 0x40741F: main (???:221)
==16284== 
==16284== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 529 from 84)
--16284-- 
--16284-- used_suppression:    527 helgrind-glibc2X-005 /usr/lib/valgrind/default.supp:945
--16284-- used_suppression:      1 helgrind-glibc2X-111 /usr/lib/valgrind/default.supp:1034
--16284-- used_suppression:      1 helgrind-glibc2X-101 /usr/lib/valgrind/default.supp:980
==16284== 
==16284== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 529 from 84)