search_23mm_phase2.c

   1 /*
   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
   6  * situations.
   7  */
   8 {
   9         bt2.setReportExacts(false);
  10
  11         if(!nofw) {
  12                 // Set up the revisitability of the halves
  13                 params.setFw(true);
  14                 bt2.setQuery(patsrc->bufa());
  15                 bt2.setOffs(0, 0, s5, s5, two? s : s5, s);
  16                 if(bt2.backtrack()) {
  17                         DONEMASK_SET(patid);
  18                         continue;
  19                 }
  20                 // if nofw is true, then we already did this
  21                 if(sink->finishedWithStratum(0)) { // no more exact hits are possible
  22                         DONEMASK_SET(patid);
  23                         continue;
  24                 }
  25         }
  26
  27         if(!norc) {
  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);
  33                 if(bt2.backtrack()) {
  34                         DONEMASK_SET(patid);
  35                         continue;
  36                 }
  37         }
  38
  39         if(nofw && sink->finishedWithStratum(1)) {
  40                 DONEMASK_SET(patid);
  41                 continue;
  42         }
  43 }