2 * This is a fragment, included from multiple places in ebwt_search.cpp.
3 * It implements the logic of the second phase of the 1-mismatch search
4 * routine. It is implemented as a code fragment so that it can be
5 * reused in both the half-index-in-memory and full-index-in-memory
10 bt.setReportExacts(false);
14 // Next, try hits with one mismatch on the 3' end for the reverse-complement read
15 bt.setQuery(patsrc->bufa());
16 bt.setOffs(0, 0, s3, s, s, s); // 1 mismatch allowed in 3' half
24 // Next, try hits with one mismatch on the 3' end for the reverse-complement read
25 bt.setQuery(patsrc->bufa());
26 bt.setOffs(0, 0, s3, s, s, s); // 1 mismatch allowed in 3' half