comparison bwa-0.6.2/bntseq.h @ 0:dd1186b11b3b draft

Uploaded BWA
author ashvark
date Fri, 18 Jul 2014 07:55:14 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:dd1186b11b3b
1 /* The MIT License
2
3 Copyright (c) 2008 Genome Research Ltd (GRL).
4
5 Permission is hereby granted, free of charge, to any person obtaining
6 a copy of this software and associated documentation files (the
7 "Software"), to deal in the Software without restriction, including
8 without limitation the rights to use, copy, modify, merge, publish,
9 distribute, sublicense, and/or sell copies of the Software, and to
10 permit persons to whom the Software is furnished to do so, subject to
11 the following conditions:
12
13 The above copyright notice and this permission notice shall be
14 included in all copies or substantial portions of the Software.
15
16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
18 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
20 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
21 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
22 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
23 SOFTWARE.
24 */
25
26 /* Contact: Heng Li <lh3@sanger.ac.uk> */
27
28 #ifndef BWT_BNTSEQ_H
29 #define BWT_BNTSEQ_H
30
31 #include <stdint.h>
32 #include <zlib.h>
33
34 #ifndef BWA_UBYTE
35 #define BWA_UBYTE
36 typedef uint8_t ubyte_t;
37 #endif
38
39 typedef struct {
40 int64_t offset;
41 int32_t len;
42 int32_t n_ambs;
43 uint32_t gi;
44 char *name, *anno;
45 } bntann1_t;
46
47 typedef struct {
48 int64_t offset;
49 int32_t len;
50 char amb;
51 } bntamb1_t;
52
53 typedef struct {
54 int64_t l_pac;
55 int32_t n_seqs;
56 uint32_t seed;
57 bntann1_t *anns; // n_seqs elements
58 int32_t n_holes;
59 bntamb1_t *ambs; // n_holes elements
60 FILE *fp_pac;
61 } bntseq_t;
62
63 extern unsigned char nst_nt4_table[256];
64
65 #ifdef __cplusplus
66 extern "C" {
67 #endif
68
69 void bns_dump(const bntseq_t *bns, const char *prefix);
70 bntseq_t *bns_restore(const char *prefix);
71 bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename);
72 void bns_destroy(bntseq_t *bns);
73 int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only);
74 int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id);
75
76 #ifdef __cplusplus
77 }
78 #endif
79
80 static inline int64_t bns_depos(const bntseq_t *bns, int64_t pos, int *is_rev)
81 {
82 return (*is_rev = (pos >= bns->l_pac))? (bns->l_pac<<1) - 1 - pos : pos;
83 }
84
85 #endif