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Searched refs:bsmpl (Results 1 – 11 of 11) sorted by relevance

/dports/biology/bcftools/bcftools-1.14/
H A D	bam_sample.c	63 return bsmpl; in bam_smpl_init() 69 if ( bsmpl->name2idx ) khash_str2int_destroy_free(bsmpl->name2idx); in bam_smpl_destroy() 82 free(bsmpl); in bam_smpl_destroy() 99 bsmpl->smpl = (char*) realloc(bsmpl->smpl,sizeof(char)bsmpl->nsmpl); in bsmpl_add_readgroup() 100 bsmpl->smpl[bsmpl->nsmpl-1] = strdup(smpl_name); in bsmpl_add_readgroup() 101 ismpl = khash_str2int_inc(bsmpl->name2idx,bsmpl->smpl[bsmpl->nsmpl-1]); in bsmpl_add_readgroup() 122 rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); in bsmpl_keep_readgroup() 129 rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); in bsmpl_keep_readgroup() 153 bsmpl->nfiles++; in bam_smpl_add_bam() 154 bsmpl->files = (file_t) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t)); in bam_smpl_add_bam() [all …]
H A D	bam_sample.h	`35 int bam_smpl_add_samples(bam_smpl_t bsmpl, char list, int is_file); 36 int bam_smpl_add_readgroups(bam_smpl_t bsmpl, char list, int is_file); 37 void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl); 43 int bam_smpl_add_bam(bam_smpl_t bsmpl, char bam_hdr, const char fname); 45 const char bam_smpl_get_samples(bam_smpl_t bsmpl, int nsmpl); 46 int bam_smpl_get_sample_id(bam_smpl_t bsmpl, int bam_id, bam1_t bam_rec); 48 void bam_smpl_destroy(bam_smpl_t bsmpl);`
H A D	mpileup.c	95 bam_smpl_t bsmpl; member 219 if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue; in mplp_func() 303 int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t )b); in pileup_constructor() 559 group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp); in mpileup_reg() 662 conf->mplp_data[i]->bam_id = bam_smpl_add_bam(conf->bsmpl,h_tmp->text,conf->files[i]); in mpileup() 715 bam_smpl_get_samples(conf->bsmpl, &conf->gplp->n); in mpileup() 834 const char **smpl = bam_smpl_get_samples(conf->bsmpl, &nsmpl); in mpileup() 1214 mplp.bsmpl = bam_smpl_init(); in main_mpileup() 1300 case 5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break; in main_mpileup() 1402 case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break; in main_mpileup() [all …]
/dports/biology/bio-mocha/bcftools-1.14/
H A D	bam_sample.c	63 return bsmpl; in bam_smpl_init() 69 if ( bsmpl->name2idx ) khash_str2int_destroy_free(bsmpl->name2idx); in bam_smpl_destroy() 82 free(bsmpl); in bam_smpl_destroy() 99 bsmpl->smpl = (char*) realloc(bsmpl->smpl,sizeof(char)bsmpl->nsmpl); in bsmpl_add_readgroup() 100 bsmpl->smpl[bsmpl->nsmpl-1] = strdup(smpl_name); in bsmpl_add_readgroup() 101 ismpl = khash_str2int_inc(bsmpl->name2idx,bsmpl->smpl[bsmpl->nsmpl-1]); in bsmpl_add_readgroup() 122 rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); in bsmpl_keep_readgroup() 129 rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); in bsmpl_keep_readgroup() 153 bsmpl->nfiles++; in bam_smpl_add_bam() 154 bsmpl->files = (file_t) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t)); in bam_smpl_add_bam() [all …]
H A D	bam_sample.h	`35 int bam_smpl_add_samples(bam_smpl_t bsmpl, char list, int is_file); 36 int bam_smpl_add_readgroups(bam_smpl_t bsmpl, char list, int is_file); 37 void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl); 43 int bam_smpl_add_bam(bam_smpl_t bsmpl, char bam_hdr, const char fname); 45 const char bam_smpl_get_samples(bam_smpl_t bsmpl, int nsmpl); 46 int bam_smpl_get_sample_id(bam_smpl_t bsmpl, int bam_id, bam1_t bam_rec); 48 void bam_smpl_destroy(bam_smpl_t bsmpl);`
H A D	mpileup.c	95 bam_smpl_t bsmpl; member 219 if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue; in mplp_func() 303 int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t )b); in pileup_constructor() 559 group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp); in mpileup_reg() 662 conf->mplp_data[i]->bam_id = bam_smpl_add_bam(conf->bsmpl,h_tmp->text,conf->files[i]); in mpileup() 715 bam_smpl_get_samples(conf->bsmpl, &conf->gplp->n); in mpileup() 834 const char **smpl = bam_smpl_get_samples(conf->bsmpl, &nsmpl); in mpileup() 1214 mplp.bsmpl = bam_smpl_init(); in main_mpileup() 1300 case 5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break; in main_mpileup() 1402 case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break; in main_mpileup() [all …]
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A D	bam_sample.c	63 return bsmpl; in bam_smpl_init() 69 if ( bsmpl->name2idx ) khash_str2int_destroy_free(bsmpl->name2idx); in bam_smpl_destroy() 82 free(bsmpl); in bam_smpl_destroy() 99 bsmpl->smpl = (char*) realloc(bsmpl->smpl,sizeof(char)bsmpl->nsmpl); in bsmpl_add_readgroup() 100 bsmpl->smpl[bsmpl->nsmpl-1] = strdup(smpl_name); in bsmpl_add_readgroup() 101 ismpl = khash_str2int_inc(bsmpl->name2idx,bsmpl->smpl[bsmpl->nsmpl-1]); in bsmpl_add_readgroup() 122 rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); in bsmpl_keep_readgroup() 129 rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); in bsmpl_keep_readgroup() 153 bsmpl->nfiles++; in bam_smpl_add_bam() 154 bsmpl->files = (file_t) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t)); in bam_smpl_add_bam() [all …]
H A D	bam_sample.c.pysam.c	65 return bsmpl; in bam_smpl_init() 71 if ( bsmpl->name2idx ) khash_str2int_destroy_free(bsmpl->name2idx); in bam_smpl_destroy() 84 free(bsmpl); in bam_smpl_destroy() 101 bsmpl->smpl = (char*) realloc(bsmpl->smpl,sizeof(char)bsmpl->nsmpl); in bsmpl_add_readgroup() 102 bsmpl->smpl[bsmpl->nsmpl-1] = strdup(smpl_name); in bsmpl_add_readgroup() 103 ismpl = khash_str2int_inc(bsmpl->name2idx,bsmpl->smpl[bsmpl->nsmpl-1]); in bsmpl_add_readgroup() 124 rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); in bsmpl_keep_readgroup() 131 rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s); in bsmpl_keep_readgroup() 155 bsmpl->nfiles++; in bam_smpl_add_bam() 156 bsmpl->files = (file_t) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t)); in bam_smpl_add_bam() [all …]
H A D	bam_sample.h	`35 int bam_smpl_add_samples(bam_smpl_t bsmpl, char list, int is_file); 36 int bam_smpl_add_readgroups(bam_smpl_t bsmpl, char list, int is_file); 37 void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl); 43 int bam_smpl_add_bam(bam_smpl_t bsmpl, char bam_hdr, const char fname); 45 const char bam_smpl_get_samples(bam_smpl_t bsmpl, int nsmpl); 46 int bam_smpl_get_sample_id(bam_smpl_t bsmpl, int bam_id, bam1_t bam_rec); 48 void bam_smpl_destroy(bam_smpl_t bsmpl);`
H A D	mpileup.c	95 bam_smpl_t bsmpl; member 219 if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue; in mplp_func() 303 int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t )b); in pileup_constructor() 559 group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp); in mpileup_reg() 662 conf->mplp_data[i]->bam_id = bam_smpl_add_bam(conf->bsmpl,h_tmp->text,conf->files[i]); in mpileup() 715 bam_smpl_get_samples(conf->bsmpl, &conf->gplp->n); in mpileup() 834 const char **smpl = bam_smpl_get_samples(conf->bsmpl, &nsmpl); in mpileup() 1214 mplp.bsmpl = bam_smpl_init(); in main_mpileup() 1300 case 5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break; in main_mpileup() 1402 case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break; in main_mpileup() [all …]
H A D	mpileup.c.pysam.c	97 bam_smpl_t bsmpl; member 221 if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue; in mplp_func() 305 int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t )b); in pileup_constructor() 561 group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp); in mpileup_reg() 664 conf->mplp_data[i]->bam_id = bam_smpl_add_bam(conf->bsmpl,h_tmp->text,conf->files[i]); in mpileup() 717 bam_smpl_get_samples(conf->bsmpl, &conf->gplp->n); in mpileup() 836 const char **smpl = bam_smpl_get_samples(conf->bsmpl, &nsmpl); in mpileup() 1216 mplp.bsmpl = bam_smpl_init(); in main_mpileup() 1302 case 5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break; in main_mpileup() 1404 case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break; in main_mpileup() [all …]