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Searched refs:nsmpl (Results 1 – 25 of 126) sorted by relevance

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/dports/biology/bcftools/bcftools-1.14/plugins/
H A Dcheck-sparsity.c44 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 …]
H A Dsplit.c173 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 …]
H A Dtag2tag.c221 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()
/dports/biology/bio-mocha/bcftools-1.14/plugins/
H A Dcheck-sparsity.c44 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 …]
H A Dsplit.c173 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 …]
H A DextendFMT.c53 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 …]
H A Dtag2tag.c221 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()
/dports/math/scilab/scilab-6.1.1/scilab/modules/cacsd/macros/
H A DfindBDK.sci1 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 …]
H A DfindABCD.sci1 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 …]
/dports/biology/bcftools/bcftools-1.14/
H A Dmcall.c258 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 …]
H A Dgvcf.c90 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()
H A Dabuf.c440 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 …]
H A Dvcfnorm.c707 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 …]
/dports/biology/bio-mocha/bcftools-1.14/
H A Dmcall.c258 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 …]
H A Dgvcf.c90 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()
H A Dabuf.c440 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 …]
H A Dvcfnorm.c707 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 …]
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dmcall.c258 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 …]
H A Dmcall.c.pysam.c260 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 …]
H A Dgvcf.c90 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()
H A Dgvcf.c.pysam.c92 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()
H A Dabuf.c440 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 …]
H A Dabuf.c.pysam.c442 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 …]
H A Dvcfnorm.c707 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 …]
H A Dvcfnorm.c.pysam.c709 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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