/* * This is a fragment, included from multiple places in ebwt_search.cpp. * It implements the logic of the first 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(&ebwtFw); bt.setReportExacts(true); if(plen < 2) { cerr << "Error: Reads must be at least 2 characters long in 1-mismatch mode" << endl; throw 1; } if(!nofw) { // First, try exact hits for the forward-oriented read params.setFw(true); bt.setQuery(patsrc->bufa()); bt.setOffs(0, 0, s, s, s, s); if(bt.backtrack()) { DONEMASK_SET(patid); continue; } } if(!norc) { params.setFw(false); // Next, try exact hits for the reverse-complement read bt.setQuery(patsrc->bufa()); bt.setOffs(0, 0, s, s, s, s); if(bt.backtrack()) { DONEMASK_SET(patid); continue; } } if(sink->finishedWithStratum(0)) { // no more exact hits are possible // the sink tells us we needn't try 1-mismatch alignments DONEMASK_SET(patid); continue; } bt.setReportExacts(false); if(!norc) { // Next, try hits with one mismatch on the 3' end for the reverse-complement read bt.setQuery(patsrc->bufa()); bt.setOffs(0, 0, s5, s, s, s); // 1 mismatch allowed in 3' half if(bt.backtrack()) { DONEMASK_SET(patid); 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, s5, s, s, s); // 1 mismatch allowed in 3' half if(bt.backtrack()) { DONEMASK_SET(patid); continue; } } }