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root/gclib/gclib/GAlnExtend.h
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# Line 444 | Line 444
444   int sl,sr;
445   int score;
446   double pid;
447 + bool strong;
448   GXEditScript* editscript;
449   CAlnGapInfo* gapinfo;
450   GXAlnInfo(const char* q, int q_l, int q_r, const char* s, int s_l, int s_r,
# Line 456 | Line 457
457      sr=s_r;
458      score=sc;
459      pid=percid;
460 +    strong=false;
461      editscript=NULL;
462      gapinfo=NULL;
463      }
# Line 740 | Line 742
742          if (adist>admax) return false;
743          return (sr>=r_boundary+badj);
744     }
745 +
746    bool validate_L(int sl, int alnlen, int admax, int badj, int alnpid, int adist) {
747          if (adist>admax) return false;
748      //left match should be more stringent (5')
# Line 753 | Line 756
756  
757    bool validate(GXAlnInfo* alninfo) {
758     int alnlen=alninfo->sr - alninfo->sl + 1;
759 <   if (alninfo->pid>90.0 && alnlen>safelen)
759 >   if (alninfo->pid>90.0 && alnlen>safelen) {
760             //special case: heavy match, could be in the middle
761 +           if (alninfo->pid>95) alninfo->strong=true;
762             return true;
763 +       }
764     int sl=alninfo->sl;
765     int sr=alninfo->sr;
766     sl--;sr--; //boundary is 0-based

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