1 /* 2 Copyright (C) 2016 Genome Research Ltd. 3 4 Author: Petr Danecek <pd3@sanger.ac.uk> 5 6 Permission is hereby granted, free of charge, to any person obtaining a copy 7 of this software and associated documentation files (the "Software"), to deal 8 in the Software without restriction, including without limitation the rights 9 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 copies of the Software, and to permit persons to whom the Software is 11 furnished to do so, subject to the following conditions: 12 13 The above copyright notice and this permission notice shall be included in 14 all copies or substantial portions of the Software. 15 16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 22 THE SOFTWARE. 23 */ 24 /* 25 Parse --samples and --samples-file 26 */ 27 28 #ifndef __SMPL_ILIST_H__ 29 #define __SMPL_ILIST_H__ 30 31 #include <htslib/vcf.h> 32 33 #define SMPL_NONE 0 // flexible error recovery 34 #define SMPL_STRICT 1 // samples must exist 35 #define SMPL_SINGLE 2 // single sample expected 36 #define SMPL_PAIR1 4 // two samples expected, the first is from the bcf hdr 37 #define SMPL_PAIR2 8 // two samples expected, the second is from the bcf hdr 38 #define SMPL_VERBOSE 16 // print warnings 39 40 typedef struct 41 { 42 char **pair; // the other sample in the pair 43 int *idx; // index to bcf_hdr_t.samples; the first (SMPL_SINGLE|SMPL_PAIR1) or second sample (SMPL_PAIR2) 44 int n; 45 } 46 smpl_ilist_t; 47 48 smpl_ilist_t *smpl_ilist_init(bcf_hdr_t *hdr, char *sample_list, int is_file, int flags); 49 smpl_ilist_t *smpl_ilist_map(bcf_hdr_t *hdr_a, bcf_hdr_t *hdr_b, int flags); 50 void smpl_ilist_destroy(smpl_ilist_t *smpl); 51 52 #endif 53