2 * This is a fragment, included from multiple places in ebwt_search.cpp.
3 * It implements the logic of the second phase of the 2/3-mismatch
4 * search routine. It is implemented as a code fragment so that it can
5 * be reused in both the half-index-in-memory and full-index-in-memory
9 bt2.setReportExacts(false);
12 // Set up the revisitability of the halves
14 bt2.setQuery(patsrc->bufa());
15 bt2.setOffs(0, 0, s5, s5, two? s : s5, s);
20 // if nofw is true, then we already did this
21 if(sink->finishedWithStratum(0)) { // no more exact hits are possible
28 // Try 2/3 backtracks in the 3' half of the reverse complement read
29 params.setFw(false); // looking at reverse complement
30 // Set up the revisitability of the halves
31 bt2.setQuery(patsrc->bufa());
32 bt2.setOffs(0, 0, s3, s3, two? s : s3, s);
39 if(nofw && sink->finishedWithStratum(1)) {