/* * This is a fragment, included from multiple places in ebwt_search.cpp. * It implements the logic of the second phase of the 1-mismatch search * routine. It is implemented as a code fragment so that it can be * reused in both the half-index-in-memory and full-index-in-memory * situations. */ { bt.setEbwt(&ebwtBw); bt.setReportExacts(false); if(!norc) { params.setFw(false); // Next, try hits with one mismatch on the 3' end for the reverse-complement read bt.setQuery(patsrc->bufa()); bt.setOffs(0, 0, s3, s, s, s); // 1 mismatch allowed in 3' half if(bt.backtrack()) { continue; } } if(!nofw) { params.setFw(true); // Next, try hits with one mismatch on the 3' end for the reverse-complement read bt.setQuery(patsrc->bufa()); bt.setOffs(0, 0, s3, s, s, s); // 1 mismatch allowed in 3' half if(bt.backtrack()) { continue; } } }