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- /* The MIT License
-
- Copyright (c) 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.
-
- */
-
- /*
- Atomize/deatomize complex variants
- */
-
- #ifndef __ABUF_H__
- #define __ABUF_H__
-
- #include <htslib/vcf.h>
-
- 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;
-
- #define abuf_set_opt(buf,type,key,value) { type tmp = value; abuf_set(buf, key, (void*)&tmp); }
- 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);
-
- #endif
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