/* * This is a fragment, included from multiple places in ebwt_search.cpp. * It implements the logic of the first 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. */ { // If requested, check that this read has the same length // as all the previous ones btr1.setReportExacts(true); if(plen < 3 && two) { cerr << "Error: Read (" << name << ") is less than 3 characters long" << endl; throw 1; } else if(plen < 4) { cerr << "Error: Read (" << name << ") is less than 4 characters long" << endl; throw 1; } if(!nofw) { // Do an exact-match search on the forward pattern, just in // case we can pick it off early here params.setFw(true); btr1.setQuery(patsrc->bufa()); btr1.setOffs(0, 0, plen, plen, plen, plen); if(btr1.backtrack()) { DONEMASK_SET(patid); continue; } } if(!norc) { // Set up backtracker with reverse complement params.setFw(false); // Set up the revisitability of the halves btr1.setQuery(patsrc->bufa()); btr1.setOffs(0, 0, s5, s5, two ? s : s5, s); if(btr1.backtrack()) { DONEMASK_SET(patid); continue; } } if(nofw && sink->finishedWithStratum(0)) { // no more exact hits are possible DONEMASK_SET(patid); continue; } }