| /* The MIT License | |
| Copyright (c) 2021 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. | |
| */ | |
| /* | |
| Atomize/deatomize complex variants | |
| */ | |
| typedef struct _abuf_t abuf_t; | |
| // Modes of operation | |
| typedef enum | |
| { | |
| NONE, | |
| // mode of operation, to be passed to abuf_init | |
| SPLIT, | |
| JOIN, | |
| BCF_HDR, // should the records be annotated, a writable bcf header is required | |
| INFO_TAG, // set BCF_HDR first | |
| STAR_ALLELE // 1: use STAR allele (the default), 0: set overlaps to missing | |
| } | |
| abuf_opt_t; | |
| void abuf_set(abuf_t *buf, abuf_opt_t key, void *value); | |
| /* | |
| * abuf_init() - init buffer | |
| * @win: number of sites (>0) or bp (<0) | |
| */ | |
| abuf_t *abuf_init(const bcf_hdr_t *hdr, abuf_opt_t mode); | |
| void abuf_destroy(abuf_t *buf); | |
| /* | |
| * abuf_push() - Push a new site for analysis | |
| */ | |
| void abuf_push(abuf_t *buf, bcf1_t *rec); | |
| /* | |
| * abuf_flush() - Return next buffered record | |
| * @flush_all: Set to 1 if no more overlapping records are coming (e.g. end of chromosome or end of file), | |
| * the buffer can be emptied. | |
| * return: The next atomized/deatomized VCF record or NULL if no record is ready. The returned | |
| * structure will be cleaned by abuf. | |
| */ | |
| bcf1_t *abuf_flush(abuf_t *buf, int flush_all); | |