/* 
    Copyright (C) 2016-2021 Genome Research Ltd.

    Author: Petr Danecek <pd3@sanger.ac.uk>

    Permission is hereby granted, free of charge, to any person obtaining a copy
    of this software and associated documentation files (the "Software"), to deal
    in the Software without restriction, including without limitation the rights
    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
    copies of the Software, and to permit persons to whom the Software is
    furnished to do so, subject to the following conditions:
    
    The above copyright notice and this permission notice shall be included in
    all copies or substantial portions of the Software.
    
    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
    THE SOFTWARE.
*/
/*
    Parse --samples and --samples-file
*/

#ifndef __SMPL_ILIST_H__
#define __SMPL_ILIST_H__

#include <htslib/vcf.h>

#define SMPL_NONE     0   // flexible error recovery
#define SMPL_STRICT   1   // samples must exist
#define SMPL_SINGLE   2   // single sample expected
#define SMPL_PAIR1    4   // two samples expected, the first is from the bcf hdr
#define SMPL_PAIR2    8   // two samples expected, the second is from the bcf hdr
#define SMPL_VERBOSE 16   // print warnings 
#define SMPL_REORDER 32   // reorder samples as asked, sample_list[i] points to the VCF header index

typedef struct
{
    char **pair;    // the other sample in the pair
    int *idx;       // index to bcf_hdr_t.samples; the first (SMPL_SINGLE|SMPL_PAIR1) or second sample (SMPL_PAIR2)
    int n;
}
smpl_ilist_t;

smpl_ilist_t *smpl_ilist_init(bcf_hdr_t *hdr, char *sample_list, int is_file, int flags);
smpl_ilist_t *smpl_ilist_map(bcf_hdr_t *hdr_a, bcf_hdr_t *hdr_b, int flags);
void smpl_ilist_destroy(smpl_ilist_t *smpl);

#endif
