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
|
/*
* This is a fragment, included from multiple places in ebwt_search.cpp.
* It implements the logic of the exact-search routine. It is
* implemented as a code fragment so that it can be reused in both
* paired and unpaired alignment.
*/
{
uint32_t plen = (uint32_t)length(patsrc->bufa().patFw);
if(!nofw) {
// Match against forward strand
params.setFw(true);
bt.setQuery(patsrc->bufa());
bt.setOffs(0, 0, plen, plen, plen, plen);
// If we matched on the forward strand, ignore the reverse-
// complement strand
if(bt.backtrack()) {
continue;
}
}
if(!norc) {
// Process reverse-complement read
params.setFw(false);
bt.setQuery(patsrc->bufa());
bt.setOffs(0, 0, plen, plen, plen, plen);
bt.backtrack();
}
}
|
