| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | mcall.c | 252 int i, nsmpl = bcf_hdr_nsamples(call->hdr); in init_sample_groups() local
597 int nsmpl = grp->nsmpl; in mcall_find_best_alleles() local
717 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_set_ref_genotypes() local
750 int nsmpl = grp->nsmpl; in mcall_call_genotypes() local
1166 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_trim_and_update_PLs() local
1242 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_trim_and_update_numberR() local
1345 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_constrain_alleles() local
1397 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_constrain_alleles() local
1437 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall() local
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| H A D | bam_sample.c | 49 int ignore_rg, nsmpl, nfiles; member
257 const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl) in bam_smpl_get_samples()
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| H A D | ccall.c | 315 int nsmpl = bcf_hdr_nsamples(call->hdr); in ccall() local
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| H A D | gvcf.c | 90 int i, ret, nsmpl = bcf_hdr_nsamples(hdr); in gvcf_write() local
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | mcall.c | 252 int i, nsmpl = bcf_hdr_nsamples(call->hdr); in init_sample_groups() local
597 int nsmpl = grp->nsmpl; in mcall_find_best_alleles() local
717 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_set_ref_genotypes() local
750 int nsmpl = grp->nsmpl; in mcall_call_genotypes() local
1166 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_trim_and_update_PLs() local
1242 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_trim_and_update_numberR() local
1345 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_constrain_alleles() local
1397 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_constrain_alleles() local
1437 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall() local
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| H A D | bam_sample.c | 49 int ignore_rg, nsmpl, nfiles; member
257 const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl) in bam_smpl_get_samples()
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| H A D | gvcf.c | 90 int i, ret, nsmpl = bcf_hdr_nsamples(hdr); in gvcf_write() local
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| H A D | ccall.c | 315 int nsmpl = bcf_hdr_nsamples(call->hdr); in ccall() local
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | mcall.c | 252 int i, nsmpl = bcf_hdr_nsamples(call->hdr); in init_sample_groups() local
597 int nsmpl = grp->nsmpl; in mcall_find_best_alleles() local
717 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_set_ref_genotypes() local
750 int nsmpl = grp->nsmpl; in mcall_call_genotypes() local
1166 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_trim_and_update_PLs() local
1242 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_trim_and_update_numberR() local
1345 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_constrain_alleles() local
1397 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_constrain_alleles() local
1437 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall() local
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| H A D | mcall.c.pysam.c | 254 int i, nsmpl = bcf_hdr_nsamples(call->hdr); in init_sample_groups() local
599 int nsmpl = grp->nsmpl; in mcall_find_best_alleles() local
719 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_set_ref_genotypes() local
752 int nsmpl = grp->nsmpl; in mcall_call_genotypes() local
1168 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_trim_and_update_PLs() local
1244 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_trim_and_update_numberR() local
1347 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_constrain_alleles() local
1399 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall_constrain_alleles() local
1439 int nsmpl = bcf_hdr_nsamples(call->hdr); in mcall() local
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| H A D | bam_sample.c | 49 int ignore_rg, nsmpl, nfiles; member
257 const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl) in bam_smpl_get_samples()
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| H A D | bam_sample.c.pysam.c | 51 int ignore_rg, nsmpl, nfiles; member
259 const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl) in bam_smpl_get_samples()
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| H A D | ccall.c | 315 int nsmpl = bcf_hdr_nsamples(call->hdr); in ccall() local
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| H A D | ccall.c.pysam.c | 317 int nsmpl = bcf_hdr_nsamples(call->hdr); in ccall() local
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| H A D | gvcf.c | 90 int i, ret, nsmpl = bcf_hdr_nsamples(hdr); in gvcf_write() local
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| /dports/biology/bcftools/bcftools-1.14/plugins/ |
| H A D | tag2tag.c | 221 int nsmpl = bcf_hdr_nsamples(in_hdr); in process() local
281 int nsmpl = bcf_hdr_nsamples(in_hdr); in process() local
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| H A D | fill-tags.c | 82 int nsmpl, *smpl; member
156 int moff = 0, *off = NULL, nsmpl = 0; in parse_samples() local
227 int i,j, nsmpl; in init_pops() local
623 int i,j, nsmpl = bcf_hdr_nsamples(args->in_hdr);; in process_fmt() local
872 int nsmpl = bcf_hdr_nsamples(args->in_hdr); in process_vaf() local
914 int nsmpl = bcf_hdr_nsamples(args->in_hdr); in process_vaf_vaf1() local
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| H A D | split.c | 50 int nsmpl, *smpl; // number of samples to keep and their indices in the input header member
170 int i,j, nsmpl = bcf_hdr_nsamples(args->hdr_in); in init_subsets() local
380 int i,j, nsmpl = bcf_hdr_nsamples(args->hdr_in); in init_data() local
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| /dports/biology/bio-mocha/bcftools-1.14/plugins/ |
| H A D | tag2tag.c | 221 int nsmpl = bcf_hdr_nsamples(in_hdr); in process() local
281 int nsmpl = bcf_hdr_nsamples(in_hdr); in process() local
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| H A D | mocha.h | 225 int nsmpl) { in bcf_get_unphased_genotype_alleles()
268 static inline int bcf_get_genotype_phase(const bcf_fmt_t *fmt, int8_t *gt_phase_arr, int nsmpl) { in bcf_get_genotype_phase()
314 int16_t *ad0_arr, int16_t *ad1_arr, int nsmpl) { in bcf_get_allelic_depth()
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| H A D | fill-tags.c | 82 int nsmpl, *smpl; member
156 int moff = 0, *off = NULL, nsmpl = 0; in parse_samples() local
227 int i,j, nsmpl; in init_pops() local
623 int i,j, nsmpl = bcf_hdr_nsamples(args->in_hdr);; in process_fmt() local
872 int nsmpl = bcf_hdr_nsamples(args->in_hdr); in process_vaf() local
914 int nsmpl = bcf_hdr_nsamples(args->in_hdr); in process_vaf_vaf1() local
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| H A D | split.c | 50 int nsmpl, *smpl; // number of samples to keep and their indices in the input header member
170 int i,j, nsmpl = bcf_hdr_nsamples(args->hdr_in); in init_subsets() local
380 int i,j, nsmpl = bcf_hdr_nsamples(args->hdr_in); in init_data() local
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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()
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| /dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
| H A D | ajvarbcf.c | 369 int ajVarbcfWrite(AjPVarBcfFile fp, ajint nsmpl, const AjPVarBcf b) in ajVarbcfWrite()
409 int ajVarbcfRead(AjPVarBcfFile fp, ajint nsmpl, AjPVarBcf b) in ajVarbcfRead()
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| /dports/math/octave-forge-control/control-3.3.1/src/ |
| H A D | sl_ib01ad.cc | 146 F77_INT nsmpl = 0; // total number of samples variable
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