1 /* The MIT License
2 
3    Copyright (c) 2021 Genome Research Ltd.
4 
5    Author: Petr Danecek <pd3@sanger.ac.uk>
6 
7    Permission is hereby granted, free of charge, to any person obtaining a copy
8    of this software and associated documentation files (the "Software"), to deal
9    in the Software without restriction, including without limitation the rights
10    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11    copies of the Software, and to permit persons to whom the Software is
12    furnished to do so, subject to the following conditions:
13 
14    The above copyright notice and this permission notice shall be included in
15    all copies or substantial portions of the Software.
16 
17    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
20    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
22    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
23    THE SOFTWARE.
24 
25  */
26 
27 /*
28     Atomize/deatomize complex variants
29 */
30 
31 #ifndef __ABUF_H__
32 #define __ABUF_H__
33 
34 #include <htslib/vcf.h>
35 
36 typedef struct _abuf_t abuf_t;
37 
38 // Modes of operation
39 typedef enum
40 {
41     NONE,
42 
43     // mode of operation, to be passed to abuf_init
44     SPLIT,
45     JOIN,
46 
47     BCF_HDR,        // should the records be annotated, a writable bcf header is required
48     INFO_TAG,       // set BCF_HDR first
49     STAR_ALLELE     // 1: use STAR allele (the default), 0: set overlaps to missing
50 }
51 abuf_opt_t;
52 
53 #define abuf_set_opt(buf,type,key,value) { type tmp = value; abuf_set(buf, key, (void*)&tmp); }
54 void abuf_set(abuf_t *buf, abuf_opt_t key, void *value);
55 
56 /*
57  *  abuf_init() - init buffer
58  *  @win:   number of sites (>0) or bp (<0)
59  */
60 abuf_t *abuf_init(const bcf_hdr_t *hdr, abuf_opt_t mode);
61 void abuf_destroy(abuf_t *buf);
62 
63 /*
64  *  abuf_push() - Push a new site for analysis
65  */
66 void abuf_push(abuf_t *buf, bcf1_t *rec);
67 
68 /*
69  *  abuf_flush() - Return next buffered record
70  *  @flush_all: Set to 1 if no more overlapping records are coming (e.g. end of chromosome or end of file),
71  *              the buffer can be emptied.
72  *  return:     The next atomized/deatomized VCF record or NULL if no record is ready. The returned
73  *              structure will be cleaned by abuf.
74  */
75 bcf1_t *abuf_flush(abuf_t *buf, int flush_all);
76 
77 #endif
78 
79