/* * This is a fragment, included from multiple places in ebwt_search.cpp. * It implements the logic of the second phase of the 2/3-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. */ { bt2.setReportExacts(false); if(!nofw) { // Set up the revisitability of the halves params.setFw(true); bt2.setQuery(patsrc->bufa()); bt2.setOffs(0, 0, s5, s5, two? s : s5, s); if(bt2.backtrack()) { DONEMASK_SET(patid); continue; } // if nofw is true, then we already did this if(sink->finishedWithStratum(0)) { // no more exact hits are possible DONEMASK_SET(patid); continue; } } if(!norc) { // Try 2/3 backtracks in the 3' half of the reverse complement read params.setFw(false); // looking at reverse complement // Set up the revisitability of the halves bt2.setQuery(patsrc->bufa()); bt2.setOffs(0, 0, s3, s3, two? s : s3, s); if(bt2.backtrack()) { DONEMASK_SET(patid); continue; } } if(nofw && sink->finishedWithStratum(1)) { DONEMASK_SET(patid); continue; } }