Created
September 26, 2013 04:22
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Simple GenomeTools program. Compiles fine, dies with segfault at runtime. Running under valgrind, it runs to completion but reports a lot of invalid access errors.
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| #define WITHOUT_CAIRO | |
| #include "genometools.h" | |
| GtFeatureNode *eden() | |
| { | |
| GtGenomeNode *gene, *mrna1, *mrna2, *mrna3, *feature; | |
| GtFeatureNode *genefn, *mrna1fn, *mrna2fn, *mrna3fn, *featurefn; | |
| GtGenomeNode *f1, *f2, *f3, *f4; | |
| GtFeatureNode *fn1, *fn2, *fn3, *fn4; | |
| GtStr *seqid = gt_str_new_cstr("ctg123"); | |
| gene = gt_feature_node_new(seqid, "gene", 1000, 9000, GT_STRAND_FORWARD); | |
| genefn = (GtFeatureNode *)gene; | |
| gt_feature_node_add_attribute(genefn, "ID", "EDEN"); | |
| mrna1 = gt_feature_node_new(seqid, "mRNA", 1050, 9000, GT_STRAND_FORWARD); | |
| mrna1fn = (GtFeatureNode *)mrna1; | |
| gt_feature_node_add_attribute(mrna1fn, "ID", "EDEN.1"); | |
| gt_feature_node_add_child(genefn, mrna1fn); | |
| mrna2 = gt_feature_node_new(seqid, "mRNA", 1050, 9000, GT_STRAND_FORWARD); | |
| mrna2fn = (GtFeatureNode *)mrna2; | |
| gt_feature_node_add_attribute(mrna2fn, "ID", "EDEN.2"); | |
| gt_feature_node_add_child(genefn, mrna2fn); | |
| mrna3 = gt_feature_node_new(seqid, "mRNA", 1300, 9000, GT_STRAND_FORWARD); | |
| mrna3fn = (GtFeatureNode *)mrna3; | |
| gt_feature_node_add_attribute(mrna3fn, "ID", "EDEN.3"); | |
| gt_feature_node_add_child(genefn, mrna3fn); | |
| feature = gt_feature_node_new(seqid, "exon", 1050, 1500, GT_STRAND_FORWARD); | |
| featurefn = (GtFeatureNode *)feature; | |
| gt_feature_node_add_child(mrna1fn, featurefn); | |
| gt_feature_node_add_child(mrna2fn, featurefn); | |
| feature = gt_feature_node_new(seqid, "exon", 1300, 1500, GT_STRAND_FORWARD); | |
| featurefn = (GtFeatureNode *)feature; | |
| gt_feature_node_add_child(mrna3fn, featurefn); | |
| feature = gt_feature_node_new(seqid, "exon", 3000, 3902, GT_STRAND_FORWARD); | |
| featurefn = (GtFeatureNode *)feature; | |
| gt_feature_node_add_child(mrna1fn, featurefn); | |
| gt_feature_node_add_child(mrna3fn, featurefn); | |
| feature = gt_feature_node_new(seqid, "exon", 5000, 5500, GT_STRAND_FORWARD); | |
| featurefn = (GtFeatureNode *)feature; | |
| gt_feature_node_add_child(mrna1fn, featurefn); | |
| gt_feature_node_add_child(mrna2fn, featurefn); | |
| gt_feature_node_add_child(mrna3fn, featurefn); | |
| feature = gt_feature_node_new(seqid, "exon", 7000, 9000, GT_STRAND_FORWARD); | |
| featurefn = (GtFeatureNode *)feature; | |
| gt_feature_node_add_child(mrna1fn, featurefn); | |
| gt_feature_node_add_child(mrna2fn, featurefn); | |
| gt_feature_node_add_child(mrna3fn, featurefn); | |
| f1 = gt_feature_node_new(seqid, "CDS", 1201, 1500, GT_STRAND_FORWARD); | |
| fn1 = (GtFeatureNode *)f1; | |
| gt_feature_node_make_multi_representative(fn1); | |
| gt_feature_node_set_multi_representative(fn1, fn1); | |
| gt_feature_node_add_child(mrna1fn, fn1); | |
| f2 = gt_feature_node_new(seqid, "CDS", 3000, 3902, GT_STRAND_FORWARD); | |
| fn2 = (GtFeatureNode *)f2; | |
| gt_feature_node_make_multi_representative(fn2); | |
| gt_feature_node_set_multi_representative(fn2, fn1); | |
| gt_feature_node_add_child(mrna1fn, fn2); | |
| f3 = gt_feature_node_new(seqid, "CDS", 5000, 5500, GT_STRAND_FORWARD); | |
| fn3 = (GtFeatureNode *)f3; | |
| gt_feature_node_make_multi_representative(fn3); | |
| gt_feature_node_set_multi_representative(fn3, fn1); | |
| gt_feature_node_add_child(mrna1fn, fn3); | |
| f4 = gt_feature_node_new(seqid, "CDS", 7000, 7600, GT_STRAND_FORWARD); | |
| fn4 = (GtFeatureNode *)f4; | |
| gt_feature_node_make_multi_representative(fn4); | |
| gt_feature_node_set_multi_representative(fn4, fn1); | |
| gt_feature_node_add_child(mrna1fn, fn4); | |
| f1 = gt_feature_node_new(seqid, "CDS", 1201, 1500, GT_STRAND_FORWARD); | |
| fn1 = (GtFeatureNode *)f1; | |
| gt_feature_node_make_multi_representative(fn1); | |
| gt_feature_node_set_multi_representative(fn1, fn1); | |
| gt_feature_node_add_child(mrna2fn, fn1); | |
| f2 = gt_feature_node_new(seqid, "CDS", 5000, 5500, GT_STRAND_FORWARD); | |
| fn2 = (GtFeatureNode *)f2; | |
| gt_feature_node_make_multi_representative(fn2); | |
| gt_feature_node_set_multi_representative(fn2, fn1); | |
| gt_feature_node_add_child(mrna2fn, fn2); | |
| f3 = gt_feature_node_new(seqid, "CDS", 7000, 7600, GT_STRAND_FORWARD); | |
| fn3 = (GtFeatureNode *)f3; | |
| gt_feature_node_make_multi_representative(fn3); | |
| gt_feature_node_set_multi_representative(fn3, fn1); | |
| gt_feature_node_add_child(mrna2fn, fn3); | |
| f1 = gt_feature_node_new(seqid, "CDS", 3301, 3902, GT_STRAND_FORWARD); | |
| fn1 = (GtFeatureNode *)f1; | |
| gt_feature_node_make_multi_representative(fn1); | |
| gt_feature_node_set_multi_representative(fn1, fn1); | |
| gt_feature_node_add_child(mrna3fn, fn1); | |
| f2 = gt_feature_node_new(seqid, "CDS", 5000, 5500, GT_STRAND_FORWARD); | |
| fn2 = (GtFeatureNode *)f2; | |
| gt_feature_node_make_multi_representative(fn2); | |
| gt_feature_node_set_multi_representative(fn2, fn1); | |
| gt_feature_node_add_child(mrna3fn, fn2); | |
| f3 = gt_feature_node_new(seqid, "CDS", 7000, 7600, GT_STRAND_FORWARD); | |
| fn3 = (GtFeatureNode *)f3; | |
| gt_feature_node_make_multi_representative(fn3); | |
| gt_feature_node_set_multi_representative(fn3, fn1); | |
| gt_feature_node_add_child(mrna3fn, fn3); | |
| gt_str_delete(seqid); | |
| return genefn; | |
| } | |
| int main() | |
| { | |
| gt_lib_init(); | |
| GtFeatureNode *fn = eden(); | |
| gt_genome_node_delete((GtGenomeNode *)fn); | |
| gt_lib_clean(); | |
| return 0; | |
| } |
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