| /* convert.h -- functions for converting between VCF/BCF and related formats. | |
| Copyright (C) 2014-2023 Genome Research Ltd. | |
| Author: Petr Danecek <[email protected]> | |
| 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. */ | |
| typedef struct _convert_t convert_t; | |
| enum convert_option | |
| { | |
| allow_undef_tags, | |
| subset_samples, | |
| force_newline, | |
| }; | |
| convert_t *convert_init(bcf_hdr_t *hdr, int *samples, int nsamples, const char *str); | |
| void convert_destroy(convert_t *convert); | |
| int convert_set_option(convert_t *convert, enum convert_option opt, ...); | |
| int convert_header(convert_t *convert, kstring_t *str); | |
| int convert_line(convert_t *convert, bcf1_t *rec, kstring_t *str); | |
| int convert_max_unpack(convert_t *convert); | |
| int convert_is_tag_used(convert_t *convert, char *tag); | |
| const char **convert_list_used_tags(convert_t *convert, int *ntags); | |