/dports/biology/bcftools/bcftools-1.14/plugins/ |
H A D | check-sparsity.c | 44 int *smpl, nsmpl, *nsites, min_sites, gt_id; member 86 args->nsmpl = bcf_hdr_nsamples(args->hdr); in init_data() 89 for (i=0; i<args->nsmpl; i++) args->smpl[i] = i; in init_data() 138 for (i=0; i<args->nsmpl; i++) in report() 140 args->nsmpl = bcf_hdr_nsamples(args->hdr); in report() 141 for (i=0; i<args->nsmpl; i++) args->smpl[i] = i; in report() 142 memset(args->nsites, 0, sizeof(int)*args->nsmpl); in report() 203 for (i=0; i<args->nsmpl; i++) in test_region() 211 if ( i+1<args->nsmpl ) in test_region() 216 args->nsmpl--; in test_region() [all …]
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H A D | split.c | 173 args->nsets = nsmpl; in init_subsets() 175 for (i=0; i<nsmpl; i++) in init_subsets() 178 set->nsmpl = 1; in init_subsets() 195 set->nsmpl = 1; in init_subsets() 249 if ( j >= set->nsmpl ) in init_subsets() 343 set->nsmpl++; in init_subsets() 346 set->smpl[set->nsmpl-1] = idx; in init_subsets() 485 for (j=0; j<set->nsmpl; j++) in init_data() 526 out->n_sample = set->nsmpl; in rec_set_info() 535 out->n_sample = set->nsmpl; in rec_set_info() [all …]
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H A D | tag2tag.c | 221 int nsmpl = bcf_hdr_nsamples(in_hdr); in process() local 222 hts_expand(int32_t,nsmpl*2,miarr,iarr); in process() 227 n /= nsmpl; in process() 228 for (i=0; i<nsmpl; i++) in process() 274 bcf_update_genotypes(out_hdr,rec,iarr,nsmpl*2); in process() 281 int nsmpl = bcf_hdr_nsamples(in_hdr); in process() local 285 …if ( n!=nsmpl ) error("Unexpected number of QR values at %s:%"PRIhts_pos"\n",bcf_seqname(in_hdr,re… in process() 287 bcf_update_format_int32(out_hdr,rec,"QS",iarr,nsmpl); in process() 293 hts_expand(int32_t,nsmpl*nals,miarr3,iarr3); in process() 300 bcf_update_format_int32(out_hdr,rec,"QS",iarr3,nals*nsmpl); in process()
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/dports/biology/bio-mocha/bcftools-1.14/plugins/ |
H A D | check-sparsity.c | 44 int *smpl, nsmpl, *nsites, min_sites, gt_id; member 86 args->nsmpl = bcf_hdr_nsamples(args->hdr); in init_data() 89 for (i=0; i<args->nsmpl; i++) args->smpl[i] = i; in init_data() 138 for (i=0; i<args->nsmpl; i++) in report() 140 args->nsmpl = bcf_hdr_nsamples(args->hdr); in report() 141 for (i=0; i<args->nsmpl; i++) args->smpl[i] = i; in report() 142 memset(args->nsites, 0, sizeof(int)*args->nsmpl); in report() 203 for (i=0; i<args->nsmpl; i++) in test_region() 211 if ( i+1<args->nsmpl ) in test_region() 216 args->nsmpl--; in test_region() [all …]
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H A D | split.c | 173 args->nsets = nsmpl; in init_subsets() 175 for (i=0; i<nsmpl; i++) in init_subsets() 178 set->nsmpl = 1; in init_subsets() 195 set->nsmpl = 1; in init_subsets() 249 if ( j >= set->nsmpl ) in init_subsets() 343 set->nsmpl++; in init_subsets() 346 set->smpl[set->nsmpl-1] = idx; in init_subsets() 485 for (j=0; j<set->nsmpl; j++) in init_data() 526 out->n_sample = set->nsmpl; in rec_set_info() 535 out->n_sample = set->nsmpl; in rec_set_info() [all …]
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H A D | extendFMT.c | 53 int nsmpl; // number of samples member 62 static auxbuf_t *auxbuf_init(int win, int nsmpl, int type, int fmt_id, int gt_id) { in auxbuf_init() argument 65 buf->nsmpl = nsmpl; in auxbuf_init() 79 buf->phase_arr = (int8_t *)malloc(buf->nsmpl * sizeof(int8_t)); in auxbuf_init() 112 if (!buf->data[curr].vals) buf->data[curr].vals = malloc(buf->nsmpl * buf->size); in auxbuf_push() 113 if (!buf->data[curr].dist) buf->data[curr].dist = (int *)malloc(buf->nsmpl * sizeof(int)); in auxbuf_push() 114 memset(buf->data[curr].dist, 0, buf->nsmpl * sizeof(int)); in auxbuf_push() 117 …id < 0) ? 0 : bcf_get_genotype_phase(bcf_get_fmt_id(line, buf->gt_id), buf->phase_arr, buf->nsmpl); in auxbuf_push() 155 memset(buf->data[curr].vals, 0, buf->nsmpl * buf->size); in auxbuf_push() 206 …id < 0) ? 0 : bcf_get_genotype_phase(bcf_get_fmt_id(line, buf->gt_id), buf->phase_arr, buf->nsmpl); in auxbuf_flush() [all …]
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H A D | tag2tag.c | 221 int nsmpl = bcf_hdr_nsamples(in_hdr); in process() local 222 hts_expand(int32_t,nsmpl*2,miarr,iarr); in process() 227 n /= nsmpl; in process() 228 for (i=0; i<nsmpl; i++) in process() 274 bcf_update_genotypes(out_hdr,rec,iarr,nsmpl*2); in process() 281 int nsmpl = bcf_hdr_nsamples(in_hdr); in process() local 285 …if ( n!=nsmpl ) error("Unexpected number of QR values at %s:%"PRIhts_pos"\n",bcf_seqname(in_hdr,re… in process() 287 bcf_update_format_int32(out_hdr,rec,"QS",iarr,nsmpl); in process() 293 hts_expand(int32_t,nsmpl*nals,miarr3,iarr3); in process() 300 bcf_update_format_int32(out_hdr,rec,"QS",iarr3,nals*nsmpl); in process()
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/dports/math/scilab/scilab-6.1.1/scilab/modules/cacsd/macros/ |
H A D | findBDK.sci | 1 function [B,D,K,Q,Ry,S,rcnd]=findBDK(s,n,l,R,A,C,meth,job,nsmpl,tol,printw) 83 if nin<9 then nsmpl = 0;end 84 if nsmpl==[] then nsmpl = 0;end 97 B = sident(meth,jobl,s,n,l,R,tol,nsmpl,A,C,printw); 99 // If job = 1 and nsmpl > 0, D means K. 100 // If job = 1 and nsmpl = 0, D means rcnd. 101 [B,D] = sident(meth,jobl,s,n,l,R,tol,nsmpl,A,C,printw); 104 // If job = 1 and nsmpl > 0, D means K, K means Q. 105 [B,D,K] = sident(meth,jobl,s,n,l,R,tol,nsmpl,A,C,printw); 107 // If job = 1 and nsmpl > 0, D means K, K means Q, Q means Ry. [all …]
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H A D | findABCD.sci | 1 function [sys,K,Q,Ry,S,rcnd]=findABCD(s,n,l,R,meth,nsmpl,tol,printw) 77 if nin<6 then nsmpl = 0;end 78 if nsmpl==[] then nsmpl = 0;end 90 [A,C,B,D] = sident(meth,job,s,n,l,R,tol,nsmpl,[],[],printw); 92 if nsmpl==0 then 94 [A,C,B,D,K] = sident(meth,job,s,n,l,R,tol,nsmpl,[],[],printw); 96 [A,C,B,D,K] = sident(meth,job,s,n,l,R,tol,nsmpl,[],[],printw); 98 [A,C,B,D,K,Q] = sident(meth,job,s,n,l,R,tol,nsmpl,[],[],printw); 100 [A,C,B,D,K,Q,Ry] = sident(meth,job,s,n,l,R,tol,nsmpl,[],[],printw); 102 [A,C,B,D,K,Q,Ry,S] = sident(meth,job,s,n,l,R,tol,nsmpl,[],[],printw); [all …]
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | mcall.c | 258 call->smpl_grp[0].nsmpl = nsmpl; in init_sample_groups() 260 for (i=0; i<nsmpl; i++) in init_sample_groups() 288 call->nsmpl_grp = nsmpl; in init_sample_groups() 290 for (i=0; i<nsmpl; i++) in init_sample_groups() 335 for (i=0; i<nsmpl; i++) in init_sample_groups() 597 int nsmpl = grp->nsmpl; in mcall_find_best_alleles() local 750 int nsmpl = grp->nsmpl; in mcall_call_genotypes() local 844 for (is=0; is<nsmpl; is++) in mcall_call_genotypes() 1246 for (j=0; j<nsmpl; j++) in mcall_trim_and_update_numberR() 1350 for (i=0; i<nsmpl; i++) in mcall_constrain_alleles() [all …]
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H A D | gvcf.c | 90 int i, ret, nsmpl = bcf_hdr_nsamples(hdr); in gvcf_write() local 109 if ( ret==nsmpl ) in gvcf_write() 112 for (i=1; i<nsmpl; i++) in gvcf_write() 158 bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl); in gvcf_write() 173 hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp); in gvcf_write() 174 memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t)); // tmp still contains DP from rec in gvcf_write() 194 for (i=0; i<nsmpl; i++) in gvcf_write() 199 if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n"); in gvcf_write() 200 for (i=0; i<nsmpl; i++) in gvcf_write()
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H A D | abuf.c | 440 if ( !nsmpl ) return; in _split_table_set_gt() 453 int max_ploidy = buf->ngt/nsmpl; in _split_table_set_gt() 455 for (i=0; i<nsmpl; i++) in _split_table_set_gt() 482 if ( !nsmpl ) return; in _split_table_set_format() 520 int nval1 = nval / nsmpl; in _split_table_set_format() 525 … else if ( len==BCF_VL_G && mtmp < num_size*nsmpl*(nval1+3) ) mtmp = num_size*nsmpl*(nval1+3); in _split_table_set_format() 530 else if ( len==BCF_VL_G && mtmp < nsmpl*(nval1+6) ) mtmp = nsmpl*(nval1+6); in _split_table_set_format() 552 for (i=0; i<nsmpl; i++) in _split_table_set_format() 571 for (i=0; i<nsmpl; i++) in _split_table_set_format() 591 for (i=0; i<nsmpl; i++) in _split_table_set_format() [all …]
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H A D | vcfnorm.c | 707 ngts /= nsmpl; in split_format_genotype() 708 for (i=0; i<nsmpl; i++) in split_format_genotype() 760 nvals /= nsmpl; \ in split_format_numeric() 790 nvals /= nsmpl; \ in split_format_numeric() 1253 ngts /= nsmpl; in merge_format_genotype() 1261 ngts2 /= nsmpl; in merge_format_genotype() 1293 for (i=1; i<nsmpl; i++) in diploid_to_haploid() 1487 nret /= nsmpl; in merge_format_string() 1502 nret /= nsmpl; in merge_format_string() 1569 for (i=0; i<nsmpl; i++) in merge_format_string() [all …]
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | mcall.c | 258 call->smpl_grp[0].nsmpl = nsmpl; in init_sample_groups() 260 for (i=0; i<nsmpl; i++) in init_sample_groups() 288 call->nsmpl_grp = nsmpl; in init_sample_groups() 290 for (i=0; i<nsmpl; i++) in init_sample_groups() 335 for (i=0; i<nsmpl; i++) in init_sample_groups() 597 int nsmpl = grp->nsmpl; in mcall_find_best_alleles() local 750 int nsmpl = grp->nsmpl; in mcall_call_genotypes() local 844 for (is=0; is<nsmpl; is++) in mcall_call_genotypes() 1246 for (j=0; j<nsmpl; j++) in mcall_trim_and_update_numberR() 1350 for (i=0; i<nsmpl; i++) in mcall_constrain_alleles() [all …]
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H A D | gvcf.c | 90 int i, ret, nsmpl = bcf_hdr_nsamples(hdr); in gvcf_write() local 109 if ( ret==nsmpl ) in gvcf_write() 112 for (i=1; i<nsmpl; i++) in gvcf_write() 158 bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl); in gvcf_write() 173 hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp); in gvcf_write() 174 memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t)); // tmp still contains DP from rec in gvcf_write() 194 for (i=0; i<nsmpl; i++) in gvcf_write() 199 if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n"); in gvcf_write() 200 for (i=0; i<nsmpl; i++) in gvcf_write()
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H A D | abuf.c | 440 if ( !nsmpl ) return; in _split_table_set_gt() 453 int max_ploidy = buf->ngt/nsmpl; in _split_table_set_gt() 455 for (i=0; i<nsmpl; i++) in _split_table_set_gt() 482 if ( !nsmpl ) return; in _split_table_set_format() 520 int nval1 = nval / nsmpl; in _split_table_set_format() 525 … else if ( len==BCF_VL_G && mtmp < num_size*nsmpl*(nval1+3) ) mtmp = num_size*nsmpl*(nval1+3); in _split_table_set_format() 530 else if ( len==BCF_VL_G && mtmp < nsmpl*(nval1+6) ) mtmp = nsmpl*(nval1+6); in _split_table_set_format() 552 for (i=0; i<nsmpl; i++) in _split_table_set_format() 571 for (i=0; i<nsmpl; i++) in _split_table_set_format() 591 for (i=0; i<nsmpl; i++) in _split_table_set_format() [all …]
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H A D | vcfnorm.c | 707 ngts /= nsmpl; in split_format_genotype() 708 for (i=0; i<nsmpl; i++) in split_format_genotype() 760 nvals /= nsmpl; \ in split_format_numeric() 790 nvals /= nsmpl; \ in split_format_numeric() 1253 ngts /= nsmpl; in merge_format_genotype() 1261 ngts2 /= nsmpl; in merge_format_genotype() 1293 for (i=1; i<nsmpl; i++) in diploid_to_haploid() 1487 nret /= nsmpl; in merge_format_string() 1502 nret /= nsmpl; in merge_format_string() 1569 for (i=0; i<nsmpl; i++) in merge_format_string() [all …]
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | mcall.c | 258 call->smpl_grp[0].nsmpl = nsmpl; in init_sample_groups() 260 for (i=0; i<nsmpl; i++) in init_sample_groups() 288 call->nsmpl_grp = nsmpl; in init_sample_groups() 290 for (i=0; i<nsmpl; i++) in init_sample_groups() 335 for (i=0; i<nsmpl; i++) in init_sample_groups() 597 int nsmpl = grp->nsmpl; in mcall_find_best_alleles() local 750 int nsmpl = grp->nsmpl; in mcall_call_genotypes() local 844 for (is=0; is<nsmpl; is++) in mcall_call_genotypes() 1246 for (j=0; j<nsmpl; j++) in mcall_trim_and_update_numberR() 1350 for (i=0; i<nsmpl; i++) in mcall_constrain_alleles() [all …]
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H A D | mcall.c.pysam.c | 260 call->smpl_grp[0].nsmpl = nsmpl; in init_sample_groups() 262 for (i=0; i<nsmpl; i++) in init_sample_groups() 290 call->nsmpl_grp = nsmpl; in init_sample_groups() 292 for (i=0; i<nsmpl; i++) in init_sample_groups() 337 for (i=0; i<nsmpl; i++) in init_sample_groups() 599 int nsmpl = grp->nsmpl; in mcall_find_best_alleles() local 752 int nsmpl = grp->nsmpl; in mcall_call_genotypes() local 846 for (is=0; is<nsmpl; is++) in mcall_call_genotypes() 1248 for (j=0; j<nsmpl; j++) in mcall_trim_and_update_numberR() 1352 for (i=0; i<nsmpl; i++) in mcall_constrain_alleles() [all …]
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H A D | gvcf.c | 90 int i, ret, nsmpl = bcf_hdr_nsamples(hdr); in gvcf_write() local 109 if ( ret==nsmpl ) in gvcf_write() 112 for (i=1; i<nsmpl; i++) in gvcf_write() 158 bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl); in gvcf_write() 173 hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp); in gvcf_write() 174 memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t)); // tmp still contains DP from rec in gvcf_write() 194 for (i=0; i<nsmpl; i++) in gvcf_write() 199 if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n"); in gvcf_write() 200 for (i=0; i<nsmpl; i++) in gvcf_write()
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H A D | gvcf.c.pysam.c | 92 int i, ret, nsmpl = bcf_hdr_nsamples(hdr); in gvcf_write() local 111 if ( ret==nsmpl ) in gvcf_write() 114 for (i=1; i<nsmpl; i++) in gvcf_write() 160 bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl); in gvcf_write() 175 hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp); in gvcf_write() 176 memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t)); // tmp still contains DP from rec in gvcf_write() 196 for (i=0; i<nsmpl; i++) in gvcf_write() 201 if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n"); in gvcf_write() 202 for (i=0; i<nsmpl; i++) in gvcf_write()
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H A D | abuf.c | 440 if ( !nsmpl ) return; in _split_table_set_gt() 453 int max_ploidy = buf->ngt/nsmpl; in _split_table_set_gt() 455 for (i=0; i<nsmpl; i++) in _split_table_set_gt() 482 if ( !nsmpl ) return; in _split_table_set_format() 520 int nval1 = nval / nsmpl; in _split_table_set_format() 525 … else if ( len==BCF_VL_G && mtmp < num_size*nsmpl*(nval1+3) ) mtmp = num_size*nsmpl*(nval1+3); in _split_table_set_format() 530 else if ( len==BCF_VL_G && mtmp < nsmpl*(nval1+6) ) mtmp = nsmpl*(nval1+6); in _split_table_set_format() 552 for (i=0; i<nsmpl; i++) in _split_table_set_format() 571 for (i=0; i<nsmpl; i++) in _split_table_set_format() 591 for (i=0; i<nsmpl; i++) in _split_table_set_format() [all …]
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H A D | abuf.c.pysam.c | 442 if ( !nsmpl ) return; in _split_table_set_gt() 455 int max_ploidy = buf->ngt/nsmpl; in _split_table_set_gt() 457 for (i=0; i<nsmpl; i++) in _split_table_set_gt() 484 if ( !nsmpl ) return; in _split_table_set_format() 522 int nval1 = nval / nsmpl; in _split_table_set_format() 527 … else if ( len==BCF_VL_G && mtmp < num_size*nsmpl*(nval1+3) ) mtmp = num_size*nsmpl*(nval1+3); in _split_table_set_format() 532 else if ( len==BCF_VL_G && mtmp < nsmpl*(nval1+6) ) mtmp = nsmpl*(nval1+6); in _split_table_set_format() 554 for (i=0; i<nsmpl; i++) in _split_table_set_format() 573 for (i=0; i<nsmpl; i++) in _split_table_set_format() 593 for (i=0; i<nsmpl; i++) in _split_table_set_format() [all …]
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H A D | vcfnorm.c | 707 ngts /= nsmpl; in split_format_genotype() 708 for (i=0; i<nsmpl; i++) in split_format_genotype() 760 nvals /= nsmpl; \ in split_format_numeric() 790 nvals /= nsmpl; \ in split_format_numeric() 1253 ngts /= nsmpl; in merge_format_genotype() 1261 ngts2 /= nsmpl; in merge_format_genotype() 1293 for (i=1; i<nsmpl; i++) in diploid_to_haploid() 1487 nret /= nsmpl; in merge_format_string() 1502 nret /= nsmpl; in merge_format_string() 1569 for (i=0; i<nsmpl; i++) in merge_format_string() [all …]
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H A D | vcfnorm.c.pysam.c | 709 ngts /= nsmpl; in split_format_genotype() 710 for (i=0; i<nsmpl; i++) in split_format_genotype() 762 nvals /= nsmpl; \ in split_format_numeric() 792 nvals /= nsmpl; \ in split_format_numeric() 1255 ngts /= nsmpl; in merge_format_genotype() 1263 ngts2 /= nsmpl; in merge_format_genotype() 1295 for (i=1; i<nsmpl; i++) in diploid_to_haploid() 1489 nret /= nsmpl; in merge_format_string() 1504 nret /= nsmpl; in merge_format_string() 1571 for (i=0; i<nsmpl; i++) in merge_format_string() [all …]
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