/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/ |
H A D | bcf_sr_sort.c | 248 vcf_buf_t *buf = &srt->vcf_buf[i]; in push_vset() 259 vcf_buf_t *buf = &srt->vcf_buf[jvcf]; in push_vset() 291 for (j=0; j<srt->vcf_buf[0].nrec; j++) in debug_vbuf() 296 vcf_buf_t *buf = &srt->vcf_buf[i]; in debug_vbuf() 356 srt->vcf_buf[ireader].nrec = 0; in bcf_sr_sort_set() 559 srt->vcf_buf = (vcf_buf_t*) realloc(srt->vcf_buf,readers->nreaders*sizeof(vcf_buf_t)); in bcf_sr_sort_next() 568 if ( !srt->vcf_buf[0].nrec ) return 0; in bcf_sr_sort_next() 575 vcf_buf_t *buf = &srt->vcf_buf[i]; in bcf_sr_sort_next() 605 free(srt->vcf_buf[i].rec); in bcf_sr_sort_remove_reader() 607 memmove(&srt->vcf_buf[i], &srt->vcf_buf[i+1], (srt->nsr - i - 1)*sizeof(vcf_buf_t)); in bcf_sr_sort_remove_reader() [all …]
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H A D | bcf_sr_sort.h | 85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
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/dports/biology/vt/vt-0.57721/lib/htslib/ |
H A D | bcf_sr_sort.c | 248 vcf_buf_t *buf = &srt->vcf_buf[i]; in push_vset() 259 vcf_buf_t *buf = &srt->vcf_buf[jvcf]; in push_vset() 296 for (j=0; j<srt->vcf_buf[0].nrec; j++) in debug_vbuf() 301 vcf_buf_t *buf = &srt->vcf_buf[i]; in debug_vbuf() 570 srt->vcf_buf = (vcf_buf_t*) realloc(srt->vcf_buf,readers->nreaders*sizeof(vcf_buf_t)); in bcf_sr_sort_next() 592 if ( !srt->vcf_buf[0].nrec ) return 0; in bcf_sr_sort_next() 601 vcf_buf_t *buf = &srt->vcf_buf[i]; in bcf_sr_sort_next() 634 if (srt->vcf_buf) in bcf_sr_sort_remove_reader() 636 free(srt->vcf_buf[i].rec); in bcf_sr_sort_remove_reader() 638 memmove(&srt->vcf_buf[i], &srt->vcf_buf[i+1], (srt->nsr - i - 1)*sizeof(vcf_buf_t)); in bcf_sr_sort_remove_reader() [all …]
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H A D | bcf_sr_sort.h | 85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
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/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/ |
H A D | bcf_sr_sort.c | 250 vcf_buf_t *buf = &srt->vcf_buf[i]; in push_vset() 261 vcf_buf_t *buf = &srt->vcf_buf[jvcf]; in push_vset() 298 for (j=0; j<srt->vcf_buf[0].nrec; j++) in debug_vbuf() 303 vcf_buf_t *buf = &srt->vcf_buf[i]; in debug_vbuf() 572 srt->vcf_buf = (vcf_buf_t*) realloc(srt->vcf_buf,readers->nreaders*sizeof(vcf_buf_t)); in bcf_sr_sort_next() 594 if ( !srt->vcf_buf[0].nrec ) return 0; in bcf_sr_sort_next() 603 vcf_buf_t *buf = &srt->vcf_buf[i]; in bcf_sr_sort_next() 636 if (srt->vcf_buf) in bcf_sr_sort_remove_reader() 638 free(srt->vcf_buf[i].rec); in bcf_sr_sort_remove_reader() 640 memmove(&srt->vcf_buf[i], &srt->vcf_buf[i+1], (srt->nsr - i - 1)*sizeof(vcf_buf_t)); in bcf_sr_sort_remove_reader() [all …]
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H A D | bcf_sr_sort.h | 85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
H A D | bcf_sr_sort.c | 238 vcf_buf_t *buf = &srt->vcf_buf[i]; in push_vset() 249 vcf_buf_t *buf = &srt->vcf_buf[jvcf]; in push_vset() 287 for (j=0; j<srt->vcf_buf[0].nrec; j++) in debug_vbuf() 292 vcf_buf_t *buf = &srt->vcf_buf[i]; in debug_vbuf() 571 srt->vcf_buf = (vcf_buf_t*) realloc(srt->vcf_buf,readers->nreaders*sizeof(vcf_buf_t)); in bcf_sr_sort_next() 593 if ( !srt->vcf_buf[0].nrec ) return 0; in bcf_sr_sort_next() 602 vcf_buf_t *buf = &srt->vcf_buf[i]; in bcf_sr_sort_next() 635 if (srt->vcf_buf) in bcf_sr_sort_remove_reader() 637 free(srt->vcf_buf[i].rec); in bcf_sr_sort_remove_reader() 639 memmove(&srt->vcf_buf[i], &srt->vcf_buf[i+1], (srt->nsr - i - 1)*sizeof(vcf_buf_t)); in bcf_sr_sort_remove_reader() [all …]
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H A D | bcf_sr_sort.h | 85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
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/dports/biology/py-pysam/pysam-0.18.0/htslib/ |
H A D | bcf_sr_sort.c | 238 vcf_buf_t *buf = &srt->vcf_buf[i]; in push_vset() 249 vcf_buf_t *buf = &srt->vcf_buf[jvcf]; in push_vset() 289 for (j=0; j<srt->vcf_buf[0].nrec; j++) in debug_vbuf() 294 vcf_buf_t *buf = &srt->vcf_buf[i]; in debug_vbuf() 593 srt->vcf_buf = (vcf_buf_t*) realloc(srt->vcf_buf,readers->nreaders*sizeof(vcf_buf_t)); in bcf_sr_sort_next() 615 if ( !srt->vcf_buf[0].nrec ) return 0; in bcf_sr_sort_next() 624 vcf_buf_t *buf = &srt->vcf_buf[i]; in bcf_sr_sort_next() 657 if (srt->vcf_buf) in bcf_sr_sort_remove_reader() 659 free(srt->vcf_buf[i].rec); in bcf_sr_sort_remove_reader() 661 memmove(&srt->vcf_buf[i], &srt->vcf_buf[i+1], (srt->nsr - i - 1)*sizeof(vcf_buf_t)); in bcf_sr_sort_remove_reader() [all …]
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H A D | bcf_sr_sort.h | 85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
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/dports/biology/htslib/htslib-1.14/ |
H A D | bcf_sr_sort.c | 238 vcf_buf_t *buf = &srt->vcf_buf[i]; in push_vset() 249 vcf_buf_t *buf = &srt->vcf_buf[jvcf]; in push_vset() 289 for (j=0; j<srt->vcf_buf[0].nrec; j++) in debug_vbuf() 294 vcf_buf_t *buf = &srt->vcf_buf[i]; in debug_vbuf() 593 srt->vcf_buf = (vcf_buf_t*) realloc(srt->vcf_buf,readers->nreaders*sizeof(vcf_buf_t)); in bcf_sr_sort_next() 615 if ( !srt->vcf_buf[0].nrec ) return 0; in bcf_sr_sort_next() 624 vcf_buf_t *buf = &srt->vcf_buf[i]; in bcf_sr_sort_next() 657 if (srt->vcf_buf) in bcf_sr_sort_remove_reader() 659 free(srt->vcf_buf[i].rec); in bcf_sr_sort_remove_reader() 661 memmove(&srt->vcf_buf[i], &srt->vcf_buf[i+1], (srt->nsr - i - 1)*sizeof(vcf_buf_t)); in bcf_sr_sort_remove_reader() [all …]
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H A D | bcf_sr_sort.h | 85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
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/dports/biology/stacks/stacks-2.4/htslib/ |
H A D | bcf_sr_sort.c | 248 vcf_buf_t *buf = &srt->vcf_buf[i]; in push_vset() 259 vcf_buf_t *buf = &srt->vcf_buf[jvcf]; in push_vset() 296 for (j=0; j<srt->vcf_buf[0].nrec; j++) in debug_vbuf() 301 vcf_buf_t *buf = &srt->vcf_buf[i]; in debug_vbuf() 570 srt->vcf_buf = (vcf_buf_t*) realloc(srt->vcf_buf,readers->nreaders*sizeof(vcf_buf_t)); in bcf_sr_sort_next() 592 if ( !srt->vcf_buf[0].nrec ) return 0; in bcf_sr_sort_next() 601 vcf_buf_t *buf = &srt->vcf_buf[i]; in bcf_sr_sort_next() 631 free(srt->vcf_buf[i].rec); in bcf_sr_sort_remove_reader() 633 memmove(&srt->vcf_buf[i], &srt->vcf_buf[i+1], (srt->nsr - i - 1)*sizeof(vcf_buf_t)); in bcf_sr_sort_remove_reader() 648 for (i=0; i<srt->nsr; i++) free(srt->vcf_buf[i].rec); in bcf_sr_sort_destroy() [all …]
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H A D | bcf_sr_sort.h | 85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | consensus.c | 98 bcf1_t **vcf_buf; member 259 args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*)); in init_data() 294 if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]); in destroy_data() 295 free(args->vcf_buf); in destroy_data() 362 return &args->vcf_buf[i]; in next_vcf_line() 386 if ( !args->vcf_buf[i] ) args->vcf_buf[i] = bcf_init1(); in unread_vcf_line() 387 bcf1_t *tmp = rec; *rec_ptr = args->vcf_buf[i]; args->vcf_buf[i] = tmp; in unread_vcf_line() 964 if ( args->vcf_rbuf.n && args->vcf_buf[args->vcf_rbuf.f]->rid==args->rid ) in consensus() 965 pos = args->vcf_buf[args->vcf_rbuf.f]->pos; in consensus()
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H A D | csq.c | 602 vbuf_t **vcf_buf; // buffered VCF lines to annotate with CSQ and flush member 1502 vbuf_t *vbuf = args->vcf_buf[i]; in destroy_data() 1515 free(args->vcf_buf); in destroy_data() 3246 if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) in vbuf_push() 3251 if ( !args->vcf_buf[i] ) args->vcf_buf[i] = (vbuf_t*) calloc(1,sizeof(vbuf_t)); in vbuf_push() 3252 args->vcf_buf[i]->n = 0; in vbuf_push() 3253 args->vcf_buf[i]->keep_until = 0; in vbuf_push() 3255 vbuf_t *vbuf = args->vcf_buf[i]; in vbuf_push() 3287 vbuf = args->vcf_buf[ args->vcf_rbuf.f ]; in vbuf_flush() 3294 vbuf = args->vcf_buf[i]; in vbuf_flush() [all …]
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | consensus.c | 98 bcf1_t **vcf_buf; member 259 args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*)); in init_data() 294 if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]); in destroy_data() 295 free(args->vcf_buf); in destroy_data() 362 return &args->vcf_buf[i]; in next_vcf_line() 386 if ( !args->vcf_buf[i] ) args->vcf_buf[i] = bcf_init1(); in unread_vcf_line() 387 bcf1_t *tmp = rec; *rec_ptr = args->vcf_buf[i]; args->vcf_buf[i] = tmp; in unread_vcf_line() 964 if ( args->vcf_rbuf.n && args->vcf_buf[args->vcf_rbuf.f]->rid==args->rid ) in consensus() 965 pos = args->vcf_buf[args->vcf_rbuf.f]->pos; in consensus()
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H A D | csq.c | 602 vbuf_t **vcf_buf; // buffered VCF lines to annotate with CSQ and flush member 1502 vbuf_t *vbuf = args->vcf_buf[i]; in destroy_data() 1515 free(args->vcf_buf); in destroy_data() 3246 if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) in vbuf_push() 3251 if ( !args->vcf_buf[i] ) args->vcf_buf[i] = (vbuf_t*) calloc(1,sizeof(vbuf_t)); in vbuf_push() 3252 args->vcf_buf[i]->n = 0; in vbuf_push() 3253 args->vcf_buf[i]->keep_until = 0; in vbuf_push() 3255 vbuf_t *vbuf = args->vcf_buf[i]; in vbuf_push() 3287 vbuf = args->vcf_buf[ args->vcf_rbuf.f ]; in vbuf_flush() 3294 vbuf = args->vcf_buf[i]; in vbuf_flush() [all …]
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | consensus.c | 98 bcf1_t **vcf_buf; member 259 args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*)); in init_data() 294 if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]); in destroy_data() 295 free(args->vcf_buf); in destroy_data() 362 return &args->vcf_buf[i]; in next_vcf_line() 386 if ( !args->vcf_buf[i] ) args->vcf_buf[i] = bcf_init1(); in unread_vcf_line() 387 bcf1_t *tmp = rec; *rec_ptr = args->vcf_buf[i]; args->vcf_buf[i] = tmp; in unread_vcf_line() 964 if ( args->vcf_rbuf.n && args->vcf_buf[args->vcf_rbuf.f]->rid==args->rid ) in consensus() 965 pos = args->vcf_buf[args->vcf_rbuf.f]->pos; in consensus()
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H A D | consensus.c.pysam.c | 100 bcf1_t **vcf_buf; member 261 args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*)); in init_data() 296 if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]); in destroy_data() 297 free(args->vcf_buf); in destroy_data() 364 return &args->vcf_buf[i]; in next_vcf_line() 388 if ( !args->vcf_buf[i] ) args->vcf_buf[i] = bcf_init1(); in unread_vcf_line() 389 bcf1_t *tmp = rec; *rec_ptr = args->vcf_buf[i]; args->vcf_buf[i] = tmp; in unread_vcf_line() 966 if ( args->vcf_rbuf.n && args->vcf_buf[args->vcf_rbuf.f]->rid==args->rid ) in consensus() 967 pos = args->vcf_buf[args->vcf_rbuf.f]->pos; in consensus()
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H A D | csq.c | 602 vbuf_t **vcf_buf; // buffered VCF lines to annotate with CSQ and flush member 1502 vbuf_t *vbuf = args->vcf_buf[i]; in destroy_data() 1515 free(args->vcf_buf); in destroy_data() 3246 if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) in vbuf_push() 3251 if ( !args->vcf_buf[i] ) args->vcf_buf[i] = (vbuf_t*) calloc(1,sizeof(vbuf_t)); in vbuf_push() 3252 args->vcf_buf[i]->n = 0; in vbuf_push() 3253 args->vcf_buf[i]->keep_until = 0; in vbuf_push() 3255 vbuf_t *vbuf = args->vcf_buf[i]; in vbuf_push() 3287 vbuf = args->vcf_buf[ args->vcf_rbuf.f ]; in vbuf_flush() 3294 vbuf = args->vcf_buf[i]; in vbuf_flush() [all …]
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H A D | csq.c.pysam.c | 604 vbuf_t **vcf_buf; // buffered VCF lines to annotate with CSQ and flush member 1504 vbuf_t *vbuf = args->vcf_buf[i]; in destroy_data() 1517 free(args->vcf_buf); in destroy_data() 3248 if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) in vbuf_push() 3253 if ( !args->vcf_buf[i] ) args->vcf_buf[i] = (vbuf_t*) calloc(1,sizeof(vbuf_t)); in vbuf_push() 3254 args->vcf_buf[i]->n = 0; in vbuf_push() 3255 args->vcf_buf[i]->keep_until = 0; in vbuf_push() 3257 vbuf_t *vbuf = args->vcf_buf[i]; in vbuf_push() 3289 vbuf = args->vcf_buf[ args->vcf_rbuf.f ]; in vbuf_flush() 3296 vbuf = args->vcf_buf[i]; in vbuf_flush() [all …]
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