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root/gclib/gclib/GAlnExtend.h
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# Line 215 | Line 215
215  
216   };
217  
218 < #define GREEDY_MAX_COST_FRACTION 5
218 > #define GREEDY_MAX_COST_FRACTION 8
219   /* (was 2) sequence_length / (this number) is a measure of how hard the
220    alignment code will work to find the optimal alignment; in fact
221    this gives a worst case bound on the number of loop iterations */
# Line 685 | Line 685
685    bool validate(int sl, int sr, int alnpid, int adist) {
686     int alnlen=sr-sl+1;
687     sl--;sr--; //boundary is 0-based
688 <   int badj=0;
689 <   int admax=3;
690 <   if (alnlen<11) {
688 >   int badj=0; //default boundary is 3 bases distance to end
689 >   int admax=1;
690 >   if (alnlen<13) {
691        //stricter boundary check
692 +      if (alnpid<90) return false;
693        badj=2;
694 <      admax=1;
694 <      if (alnlen<=6) { badj++; admax=0; }
694 >      if (alnlen<=7) { badj++; admax=0; }
695        }
696     if (adist>admax) return false;
697     if (type==galn_TrimRight) {
698        return (sr>=boundary+badj);
699        }
700     else {
701 <      //left side should be more stringent
702 <      if (alnpid<91) {
703 <        if (alnlen<11) return false;
701 >      //left match should be more stringent (5')
702 >      if (alnpid<93) {
703 >        if (alnlen<13) return false;
704 >        admax=0;
705          badj++;
706          }
707        return (sl<=boundary-badj);

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