1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef BAM_LOAD_REFERENCE_WRITER_H_
#define BAM_LOAD_REFERENCE_WRITER_H_ 1
#include <vdb/manager.h>
#include <vdb/database.h>
#include <klib/data-buffer.h>
#include <align/writer-reference.h>
#include "alignment-writer.h"
typedef struct s_reference {
const ReferenceMgr *mgr;
const ReferenceSeq *rseq;
int64_t lastRefId;
unsigned curPos;
unsigned endPos;
unsigned length;
unsigned last_id; /* == ref_info.elem_count if no last id */
KDataBuffer coverage;
KDataBuffer mismatches;
KDataBuffer indels;
KDataBuffer pri_align;
KDataBuffer sec_align;
KDataBuffer pri_overlap;
KDataBuffer sec_overlap;
KDataBuffer ref_names;
KDataBuffer ref_info;
bool out_of_order;
} Reference;
rc_t ReferenceInit(Reference *self, const VDBManager *mgr, VDatabase *db);
rc_t ReferenceSetFile(Reference *self, char const id[],
uint64_t length, uint8_t const md5[16],
bool *shouldUnmap,
bool *wasRenamed);
rc_t ReferenceVerify(Reference const *self, char const id[], uint64_t length, uint8_t const md5[16]);
rc_t ReferenceGet1stRow(Reference const *self, int64_t *refID, char const refName[]);
rc_t ReferenceAddAlignId(Reference *self,
int64_t align_id,
bool is_primary
);
rc_t ReferenceRead(Reference *self, AlignmentRecord *data, uint64_t pos,
uint32_t const rawCigar[], uint32_t cigCount,
char const seqDNA[], uint32_t seqLen,
uint8_t rna_orient, uint32_t *matches, uint32_t *misses);
rc_t ReferenceWhack(Reference *self, bool commit);
#endif
|
