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
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
|
/* bam_color.c -- color-space support.
Copyright (C) 2009, 2012 University of California - Los Angeles.
Author: Nils Homer <nilshomer@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
#include <config.h>
#include <ctype.h>
#include "bam.h"
/*!
@abstract Get the color encoding the previous and current base
@param b pointer to an alignment
@param i The i-th position, 0-based
@return color
@discussion Returns 0 no color information is found.
*/
char bam_aux_getCSi(bam1_t *b, int i)
{
uint8_t *c = bam_aux_get(b, "CS");
char *cs = NULL;
// return the base if the tag was not found
if(0 == c) return 0;
cs = bam_aux2Z(c);
// adjust for strandedness and leading adaptor
if(bam1_strand(b)) {
i = strlen(cs) - 1 - i;
// adjust for leading hard clip
uint32_t cigar = bam1_cigar(b)[0];
if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
i -= cigar >> BAM_CIGAR_SHIFT;
}
} else { i++; }
return cs[i];
}
/*!
@abstract Get the color quality of the color encoding the previous and current base
@param b pointer to an alignment
@param i The i-th position, 0-based
@return color quality
@discussion Returns 0 no color information is found.
*/
char bam_aux_getCQi(bam1_t *b, int i)
{
uint8_t *c = bam_aux_get(b, "CQ");
char *cq = NULL;
// return the base if the tag was not found
if(0 == c) return 0;
cq = bam_aux2Z(c);
// adjust for strandedness
if(bam1_strand(b)) {
i = strlen(cq) - 1 - i;
// adjust for leading hard clip
uint32_t cigar = bam1_cigar(b)[0];
if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
i -= (cigar >> BAM_CIGAR_SHIFT);
}
}
return cq[i];
}
char bam_aux_nt2int(char a)
{
switch(toupper(a)) {
case 'A':
return 0;
break;
case 'C':
return 1;
break;
case 'G':
return 2;
break;
case 'T':
return 3;
break;
default:
return 4;
break;
}
}
char bam_aux_ntnt2cs(char a, char b)
{
a = bam_aux_nt2int(a);
b = bam_aux_nt2int(b);
if(4 == a || 4 == b) return '4';
return "0123"[(int)(a ^ b)];
}
/*!
@abstract Get the color error profile at the give position
@param b pointer to an alignment
@return the original color if the color was an error, '-' (dash) otherwise
@discussion Returns 0 no color information is found.
*/
char bam_aux_getCEi(bam1_t *b, int i)
{
int cs_i;
uint8_t *c = bam_aux_get(b, "CS");
char *cs = NULL;
char prev_b, cur_b;
char cur_color, cor_color;
// return the base if the tag was not found
if(0 == c) return 0;
cs = bam_aux2Z(c);
// adjust for strandedness and leading adaptor
if(bam1_strand(b)) { //reverse strand
cs_i = strlen(cs) - 1 - i;
// adjust for leading hard clip
uint32_t cigar = bam1_cigar(b)[0];
if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
cs_i -= cigar >> BAM_CIGAR_SHIFT;
}
// get current color
cur_color = cs[cs_i];
// get previous base. Note: must rc adaptor
prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
// get current base
cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
}
else {
cs_i=i+1;
// get current color
cur_color = cs[cs_i];
// get previous base
prev_b = (0 == i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i-1)];
// get current base
cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
}
// corrected color
cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
if(cur_color == cor_color) {
return '-';
}
else {
return cur_color;
}
}
|
