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root/gclib/gclib/GAlnExtend.h
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# Line 588 | Line 588
588   class GXBandSet:public GList<GXBand> {
589    public:
590     GXSeed* qmatch; //long match (mismatches allowed) if a very good match was extended well
591 +   GXSeed* tmatch; //terminal match to be used if there is no better alignment
592     int idxoffset; //global anti-diagonal->index offset (a_len-1)
593     //used to convert a diagonal to an index
594     //diagonal is always b_ofs-a_ofs, so the minimum value is -a_len+1
# Line 601 | Line 602
602     GXBandSet(int a_len, int b_len):GList<GXBand>(a_len+b_len-1, false, true, false) {
603        idxoffset=a_len-1;
604        qmatch=NULL;
605 +      tmatch=NULL; //terminal match to be used if everything else fails
606            //diag will range from -a_len+1 to b_len-1, so after adjustment
607            //by idxoffset we get a max of a_len+b_len-2
608        int bcount=a_len+b_len-1;
# Line 689 | Line 691
691        //stricter boundary check
692        badj=2;
693        admax=1;
694 +      if (alnlen<=6) badj++;
695        }
696     if (adist>admax) return false;
697     if (type==galn_TrimRight) {

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