1 /* bam_sample.h -- group data by sample. 2 3 Copyright (C) 2010 Broad Institute. 4 Copyright (C) 2016 Genome Research Ltd. 5 6 Author: Heng Li <lh3@sanger.ac.uk>, Petr Danecek <pd3@sanger.ac.uk> 7 8 Permission is hereby granted, free of charge, to any person obtaining a copy 9 of this software and associated documentation files (the "Software"), to deal 10 in the Software without restriction, including without limitation the rights 11 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 12 copies of the Software, and to permit persons to whom the Software is 13 furnished to do so, subject to the following conditions: 14 15 The above copyright notice and this permission notice shall be included in 16 all copies or substantial portions of the Software. 17 18 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 19 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 21 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 23 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 24 DEALINGS IN THE SOFTWARE. */ 25 26 #ifndef BAM_SAMPLE_H 27 #define BAM_SAMPLE_H 28 29 #include <htslib/sam.h> 30 31 typedef struct _bam_smpl_t bam_smpl_t; 32 33 bam_smpl_t *bam_smpl_init(void); 34 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); 38 39 // The above should be called only before bams are added. Returns the BAM id 40 // to be passed to bam_smpl_get_sample_id() later. It is safe to assume 41 // sequential numbering, starting from 0. 42 // 43 int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname); 44 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); 47 48 void bam_smpl_destroy(bam_smpl_t *bsmpl); 49 50 #endif 51