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comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtaln.h @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 #ifndef BWTALN_H
2 #define BWTALN_H
3
4 #include <stdint.h>
5 #include "bwt.h"
6
7 #define BWA_TYPE_NO_MATCH 0
8 #define BWA_TYPE_UNIQUE 1
9 #define BWA_TYPE_REPEAT 2
10 #define BWA_TYPE_MATESW 3
11
12 #define SAM_FPD 1 // paired
13 #define SAM_FPP 2 // properly paired
14 #define SAM_FSU 4 // self-unmapped
15 #define SAM_FMU 8 // mate-unmapped
16 #define SAM_FSR 16 // self on the reverse strand
17 #define SAM_FMR 32 // mate on the reverse strand
18 #define SAM_FR1 64 // this is read one
19 #define SAM_FR2 128 // this is read two
20 #define SAM_FSC 256 // secondary alignment
21
22 #define BWA_AVG_ERR 0.02
23 #define BWA_MIN_RDLEN 35 // for read trimming
24
25 #ifndef bns_pac
26 #define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
27 #endif
28
29 typedef struct {
30 bwtint_t w;
31 int bid;
32 } bwt_width_t;
33
34 typedef struct {
35 uint32_t n_mm:8, n_gapo:8, n_gape:8, a:1;
36 bwtint_t k, l;
37 int score;
38 } bwt_aln1_t;
39
40 typedef uint16_t bwa_cigar_t;
41 /* rgoya: If changing order of bytes, beware of operations like:
42 * s->cigar[0] += s->full_len - s->len;
43 */
44 #define CIGAR_OP_SHIFT 14
45 #define CIGAR_LN_MASK 0x3fff
46
47 #define __cigar_op(__cigar) ((__cigar)>>CIGAR_OP_SHIFT)
48 #define __cigar_len(__cigar) ((__cigar)&CIGAR_LN_MASK)
49 #define __cigar_create(__op, __len) ((__op)<<CIGAR_OP_SHIFT | (__len))
50
51 typedef struct {
52 uint32_t pos;
53 uint32_t n_cigar:15, gap:8, mm:8, strand:1;
54 bwa_cigar_t *cigar;
55 } bwt_multi1_t;
56
57 typedef struct {
58 char *name;
59 ubyte_t *seq, *rseq, *qual;
60 uint32_t len:20, strand:1, type:2, dummy:1, extra_flag:8;
61 uint32_t n_mm:8, n_gapo:8, n_gape:8, mapQ:8;
62 int score;
63 int clip_len;
64 // alignments in SA coordinates
65 int n_aln;
66 bwt_aln1_t *aln;
67 // multiple hits
68 int n_multi;
69 bwt_multi1_t *multi;
70 // alignment information
71 bwtint_t sa, pos;
72 uint64_t c1:28, c2:28, seQ:8; // number of top1 and top2 hits; single-end mapQ
73 int n_cigar;
74 bwa_cigar_t *cigar;
75 // for multi-threading only
76 int tid;
77 // NM and MD tags
78 uint32_t full_len:20, nm:12;
79 char *md;
80 } bwa_seq_t;
81
82 #define BWA_MODE_GAPE 0x01
83 #define BWA_MODE_COMPREAD 0x02
84 #define BWA_MODE_LOGGAP 0x04
85 #define BWA_MODE_NONSTOP 0x10
86
87 typedef struct {
88 int s_mm, s_gapo, s_gape;
89 int mode;
90 int indel_end_skip, max_del_occ, max_entries;
91 float fnr;
92 int max_diff, max_gapo, max_gape;
93 int max_seed_diff, seed_len;
94 int n_threads;
95 int max_top2;
96 int trim_qual;
97 } gap_opt_t;
98
99 #define BWA_PET_STD 1
100 #define BWA_PET_SOLID 2
101
102 typedef struct {
103 int max_isize;
104 int max_occ;
105 int n_multi, N_multi;
106 int type, is_sw, is_preload;
107 double ap_prior;
108 } pe_opt_t;
109
110 struct __bwa_seqio_t;
111 typedef struct __bwa_seqio_t bwa_seqio_t;
112
113 #ifdef __cplusplus
114 extern "C" {
115 #endif
116
117 gap_opt_t *gap_init_opt();
118 void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt);
119
120 bwa_seqio_t *bwa_seq_open(const char *fn);
121 void bwa_seq_close(bwa_seqio_t *bs);
122 void seq_reverse(int len, ubyte_t *seq, int is_comp);
123 bwa_seq_t *bwa_read_seq(bwa_seqio_t *seq, int n_needed, int *n, int is_comp, int trim_qual);
124 void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs);
125
126 int bwa_cal_maxdiff(int l, double err, double thres);
127 void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt[2], int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt);
128
129 void bwa_cs2nt_core(bwa_seq_t *p, bwtint_t l_pac, ubyte_t *pac);
130
131
132 /* rgoya: Temporary clone of aln_path2cigar to accomodate for bwa_cigar_t,
133 __cigar_op and __cigar_len while keeping stdaln stand alone */
134 #include "stdaln.h"
135
136 bwa_cigar_t *bwa_aln_path2cigar(const path_t *path, int path_len, int *n_cigar);
137
138 #ifdef __cplusplus
139 }
140 #endif
141
142 #endif