/* * This is a fragment, included from multiple places in ebwt_search.cpp. * It implements the logic of the third 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(!nofw) { // Try 2/3 backtracks in the 3' half of the forward read params.setFw(true); bt3.setReportExacts(false); bt3.setQuery(patsrc->bufa()); bt3.setOffs(0, 0, s3, s3, two? s : s3, s); bool done = bt3.backtrack(); if(done) continue; // no more 1-mismatch hits are possible after this point if(sink->finishedWithStratum(1)) { continue; } // Try a half-and-half on the forward read bool gaveUp = false; bthh3.setQuery(patsrc->bufa()); // Processing the forward pattern with the forward index; // s3 ("lo") half is on the right bthh3.setOffs(s3, s, 0, two ? s3 : 0, two ? s : s3, s); done = bthh3.backtrack(); if(bthh3.numBacktracks() == bthh3.maxBacktracks()) { gaveUp = true; } bthh3.resetNumBacktracks(); if(done) { continue; } } if(!norc) { // Try a half-and-half on the reverse complement read bool gaveUp = false; params.setFw(false); bthh3.setQuery(patsrc->bufa()); // Processing the forward pattern with the forward index; // s5 ("hi") half is on the right bthh3.setOffs(s5, s, 0, two ? s5 : 0, two ? s : s5, s); bool done = bthh3.backtrack(); if(bthh3.numBacktracks() == bthh3.maxBacktracks()) { gaveUp = true; } bthh3.resetNumBacktracks(); if(done) { continue; } } }