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Searched refs:vcf_buf (Results 1 – 22 of 22) sorted by relevance

/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/
H A Dbcf_sr_sort.c248 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()
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H A Dbcf_sr_sort.h85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
/dports/biology/vt/vt-0.57721/lib/htslib/
H A Dbcf_sr_sort.c248 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()
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H A Dbcf_sr_sort.h85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/
H A Dbcf_sr_sort.c250 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()
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H A Dbcf_sr_sort.h85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/
H A Dbcf_sr_sort.c238 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()
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H A Dbcf_sr_sort.h85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
/dports/biology/py-pysam/pysam-0.18.0/htslib/
H A Dbcf_sr_sort.c238 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()
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H A Dbcf_sr_sort.h85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
/dports/biology/htslib/htslib-1.14/
H A Dbcf_sr_sort.c238 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()
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H A Dbcf_sr_sort.h85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
/dports/biology/stacks/stacks-2.4/htslib/
H A Dbcf_sr_sort.c248 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()
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H A Dbcf_sr_sort.h85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF member
/dports/biology/bio-mocha/bcftools-1.14/
H A Dconsensus.c98 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()
H A Dcsq.c602 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()
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/dports/biology/bcftools/bcftools-1.14/
H A Dconsensus.c98 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()
H A Dcsq.c602 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()
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dconsensus.c98 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()
H A Dconsensus.c.pysam.c100 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()
H A Dcsq.c602 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()
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H A Dcsq.c.pysam.c604 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()
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