Mercurial > repos > siyuan > prada

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:acc2ca1a3ba4
1 /* The MIT License
2
3 Copyright (c) 2003-2006, 2008, by Heng Li <lh3lh3@gmail.com>
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 /*
27 2009-07-23, 0.10.0
28
29 - Use 32-bit to store CIGAR
30
31 - Report suboptimal aligments
32
33 - Implemented half-fixed-half-open DP
34
35 2009-04-26, 0.9.10
36
37 - Allow to set a threshold for local alignment
38
39 2009-02-18, 0.9.9
40
41 - Fixed a bug when no residue matches
42
43 2008-08-04, 0.9.8
44
45 - Fixed the wrong declaration of aln_stdaln_aux()
46
47 - Avoid 0 coordinate for global alignment
48
49 2008-08-01, 0.9.7
50
51 - Change gap_end penalty to 5 in aln_param_bwa
52
53 - Add function to convert path_t to the CIGAR format
54
55 2008-08-01, 0.9.6
56
57 - The first gap now costs (gap_open+gap_ext), instead of
58 gap_open. Scoring systems are modified accordingly.
59
60 - Gap end is now correctly handled. Previously it is not correct.
61
62 - Change license to MIT.
63
64 */
65
66 #ifndef LH3_STDALN_H_
67 #define LH3_STDALN_H_
68
69
70 #define STDALN_VERSION 0.11.0
71
72 #include <stdint.h>
73
74 #define FROM_M 0
75 #define FROM_I 1
76 #define FROM_D 2
77 #define FROM_S 3
78
79 #define ALN_TYPE_LOCAL 0
80 #define ALN_TYPE_GLOBAL 1
81 #define ALN_TYPE_EXTEND 2
82
83 /* This is the smallest integer. It might be CPU-dependent in very RARE cases. */
84 #define MINOR_INF -1073741823
85
86 typedef struct
87 {
88 int gap_open;
89 int gap_ext;
90 int gap_end;
91
92 int *matrix;
93 int row;
94 int band_width;
95 } AlnParam;
96
97 typedef struct
98 {
99 int i, j;
100 unsigned char ctype;
101 } path_t;
102
103 typedef struct
104 {
105 path_t *path; /* for advanced users... :-) */
106 int path_len; /* for advanced users... :-) */
107 int start1, end1; /* start and end of the first sequence, coordinations are 1-based */
108 int start2, end2; /* start and end of the second sequence, coordinations are 1-based */
109 int score, subo; /* score */
110
111 char *out1, *out2; /* print them, and then you will know */
112 char *outm;
113
114 int n_cigar;
115 uint32_t *cigar32;
116 } AlnAln;
117
118 #ifdef __cplusplus
119 extern "C" {
120 #endif
121
122 AlnAln *aln_stdaln_aux(const char *seq1, const char *seq2, const AlnParam *ap,
123 int type, int do_align, int len1, int len2);
124 AlnAln *aln_stdaln(const char *seq1, const char *seq2, const AlnParam *ap, int type, int do_align);
125 void aln_free_AlnAln(AlnAln *aa);
126
127 int aln_global_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
128 path_t *path, int *path_len);
129 int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
130 path_t *path, int *path_len, int _thres, int *_subo);
131 int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
132 path_t *path, int *path_len, int G0, uint8_t *_mem);
133 uint16_t *aln_path2cigar(const path_t *path, int path_len, int *n_cigar);
134 uint32_t *aln_path2cigar32(const path_t *path, int path_len, int *n_cigar);
135
136 #ifdef __cplusplus
137 }
138 #endif
139
140 /********************
141 * global variables *
142 ********************/
143
144 extern AlnParam aln_param_bwa; /* = { 37, 9, 0, aln_sm_maq, 5, 50 }; */
145 extern AlnParam aln_param_blast; /* = { 5, 2, 2, aln_sm_blast, 5, 50 }; */
146 extern AlnParam aln_param_nt2nt; /* = { 10, 2, 2, aln_sm_nt, 16, 75 }; */
147 extern AlnParam aln_param_aa2aa; /* = { 20, 19, 19, aln_sm_read, 16, 75 }; */
148 extern AlnParam aln_param_rd2rd; /* = { 12, 2, 2, aln_sm_blosum62, 22, 50 }; */
149
150 /* common nucleotide score matrix for 16 bases */
151 extern int aln_sm_nt[];
152
153 /* BLOSUM62 and BLOSUM45 */
154 extern int aln_sm_blosum62[], aln_sm_blosum45[];
155
156 /* common read for 16 bases. note that read alignment is quite different from common nucleotide alignment */
157 extern int aln_sm_read[];
158
159 /* human-mouse score matrix for 4 bases */
160 extern int aln_sm_hs[];
161
162 #endif