2 * This is a fragment, included from multiple places in ebwt_search.cpp.
3 * It implements the logic of the exact-search routine. It is
4 * implemented as a code fragment so that it can be reused in both
5 * paired and unpaired alignment.
8 uint32_t plen = length(patsrc->bufa().patFw);
10 // Match against forward strand
12 bt.setQuery(patsrc->bufa());
13 bt.setOffs(0, 0, plen, plen, plen, plen);
14 // If we matched on the forward strand, ignore the reverse-
21 // Process reverse-complement read
23 bt.setQuery(patsrc->bufa());
24 bt.setOffs(0, 0, plen, plen, plen, plen);