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
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
|
#include "BAMfunctions.h"
#include <htslib/kstring.h>
string bam_cigarString (bam1_t *b) {//output CIGAR string
// kstring_t strK;
// kstring_t *str=&strK;
const bam1_core_t *c = &b->core;
string cigarString("");
if ( c->n_cigar > 0 ) {
uint32_t *cigar = bam_get_cigar(b);
for (int i = 0; i < c->n_cigar; ++i) {
cigarString+=to_string((uint)bam_cigar_oplen(cigar[i]))+bam_cigar_opchr(cigar[i]);
};
};
// if (c->n_cigar) { // cigar
// for (int i = 0; i < c->n_cigar; ++i) {
// kputw(bam_cigar_oplen(cigar[i]), str);
// kputc(bam_cigar_opchr(cigar[i]), str);
// }
// } else kputc('*', str);
//
// string cigarString (str->s,str->l);
return cigarString;
};
int bam_read1_fromArray(char *bamChar, bam1_t *b) //modified from samtools bam_read1 to assign BAM record in mmemry to bam structure
{
bam1_core_t *c = &b->core;
int32_t block_len; //, ret, i;
// // uint32_t x[8];
// // if ((ret = bgzf_read(fp, &block_len, 4)) != 4) {
// // if (ret == 0) return -1; // normal end-of-file
// // else return -2; // truncated
// // }
uint32_t *x;
uint32_t *bamU32=(uint32_t*) bamChar;
block_len=bamU32[0];
// // if (bgzf_read(fp, x, 32) != 32) return -3;
// // if (fp->is_be) {
// // ed_swap_4p(&block_len);
// // for (i = 0; i < 8; ++i) ed_swap_4p(x + i);
// // }
x=bamU32+1;
c->tid = x[0]; c->pos = x[1];
c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
c->l_qseq = x[4];
c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
b->l_data = block_len - 32;
if (b->l_data < 0 || c->l_qseq < 0) return -4;
if ((char *)bam_get_aux(b) - (char *)b->data > b->l_data)
return -4;
if (b->m_data < b->l_data) {
b->m_data = b->l_data;
kroundup32(b->m_data);
// no need to realloc b->data, because it is overwritten later with bamChar
// b->data = (uint8_t*)realloc(b->data, b->m_data);
// if (!b->data)
// return -4;
}
// // if (bgzf_read(fp, b->data, b->l_data) != b->l_data) return -4;
// // //b->l_aux = b->l_data - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
// // if (fp->is_be) swap_data(c, b->l_data, b->data, 0);
b->data=(uint8_t*) bamChar+4*9;
return 4 + block_len;
}
void outBAMwriteHeader (BGZF* fp, const string &samh, const vector <string> &chrn, const vector <uint> &chrl) {
bgzf_write(fp,"BAM\001",4);
int32 hlen=samh.size();
bgzf_write(fp,(char*) &hlen,sizeof(hlen));
bgzf_write(fp,samh.c_str(),hlen);
int32 nchr=(int32) chrn.size();
bgzf_write(fp,(char*) &nchr,sizeof(nchr));
for (int32 ii=0;ii<nchr;ii++) {
int32 rlen = (int32) (chrn.at(ii).size()+1);
int32 slen = (int32) chrl[ii];
bgzf_write(fp,(char*) &rlen,sizeof(rlen));
bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string
bgzf_write(fp,(char*) &slen,sizeof(slen));
};
bgzf_flush(fp);
};
// calculate bin given an alignment covering [beg,end) (zero-based, half-close-half-open)
int reg2bin(int beg, int end)
{
--end;
if (beg>>14 == end>>14) return ((1<<15)-1)/7 + (beg>>14);
if (beg>>17 == end>>17) return ((1<<12)-1)/7 + (beg>>17);
if (beg>>20 == end>>20) return ((1<<9)-1)/7 + (beg>>20);
if (beg>>23 == end>>23) return ((1<<6)-1)/7 + (beg>>23);
if (beg>>26 == end>>26) return ((1<<3)-1)/7 + (beg>>26);
return 0;
};
int bamAttrArrayWrite(int32 attr, const char* tagName, char* attrArray ) {
attrArray[0]=tagName[0];attrArray[1]=tagName[1];
attrArray[2]='i';
*( (int32*) (attrArray+3))=attr;
return 3+sizeof(int32);
};
int bamAttrArrayWrite(float attr, const char* tagName, char* attrArray ) {
attrArray[0]=tagName[0];attrArray[1]=tagName[1];
attrArray[2]='f';
*( (float*) (attrArray+3))=attr;
return 3+sizeof(int32);
};
int bamAttrArrayWrite(char attr, const char* tagName, char* attrArray ) {
attrArray[0]=tagName[0];attrArray[1]=tagName[1];
attrArray[2]='A';
attrArray[3]=attr;
return 3+sizeof(char);
};
int bamAttrArrayWrite(string &attr, const char* tagName, char* attrArray ) {
attrArray[0]=tagName[0];attrArray[1]=tagName[1];
attrArray[2]='Z';
memcpy(attrArray+3,attr.c_str(),attr.size()+1);//copy string data including \0
return 3+attr.size()+1;
};
int bamAttrArrayWrite(const vector<char> &attr, const char* tagName, char* attrArray ) {
attrArray[0]=tagName[0];attrArray[1]=tagName[1];
attrArray[2]='B';
attrArray[3]='c';
*( (int32*) (attrArray+4))=attr.size();
memcpy(attrArray+4+sizeof(int32),attr.data(),attr.size());//copy array data
return 4+sizeof(int32)+attr.size();
};
int bamAttrArrayWrite(const vector<int32> &attr, const char* tagName, char* attrArray ) {
attrArray[0]=tagName[0];attrArray[1]=tagName[1];
attrArray[2]='B';
attrArray[3]='i';
*( (int32*) (attrArray+4))=attr.size();
memcpy(attrArray+4+sizeof(int32),attr.data(),sizeof(int32)*attr.size());//copy array data
return 4+sizeof(int32)+sizeof(int32)*attr.size();
};
int bamAttrArrayWriteSAMtags(string &attrStr, char *attrArray, Parameters &P) {//write bam record into attrArray for string attribute attString
size_t pos1=0, pos2=0;
int nattr=0;
do {//cycle over multiple tags separated by tab
pos2 = attrStr.find('\t',pos1);
string attr1 = attrStr.substr(pos1, pos2-pos1); //substring containing one tag
pos1=pos2+1; //for the next search
if (attr1.empty())
continue; //extra tab at the beginning, or consecutive tabs
uint16_t tagn = * ( (uint16_t*) attr1.c_str() );
if ( !P.readFiles.samAttrKeepAll && P.readFiles.samAttrKeep.count(tagn)==0 )
continue; //skip tags not contained the list
switch (attr1.at(3)) {//TODO: support other tag types (vector tags)
case 'i':
{
int32 a1=stol(attr1.substr(5));
nattr += bamAttrArrayWrite(a1,attr1.c_str(),attrArray+nattr);
break;
};
case 'A':
{
char a1=attr1.at(5);
nattr += bamAttrArrayWrite(a1,attr1.c_str(),attrArray+nattr);
break;
};
break;
case 'Z':
{
string a1=attr1.substr(5);
nattr += bamAttrArrayWrite(a1,attr1.c_str(),attrArray+nattr);
break;
};
case 'f':
{
float a1=stof(attr1.substr(5));
nattr += bamAttrArrayWrite(a1,attr1.c_str(),attrArray+nattr);
break;
};
};
} while (pos2 != string::npos);
return nattr;
};
|
