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root/gclib/gclib/GAlnExtend.h
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# Line 597 | Line 597
597            //by idxoffset we get a max of a_len+b_len-2
598        int bcount=a_len+b_len-1;
599        for (int i=0;i<bcount;i++)
600 <                   this->Add(new GXBand(i-idxoffset));
600 >              this->Add(new GXBand(i-idxoffset));
601             //unsorted, this should set fList[i]
602        }
603     ~GXBandSet() {
# Line 677 | Line 677
677      prepare(trim_type, s, s_len);
678      }
679  
680 <  bool validate(int sl, int sr, int alnpid, int adist) {
680 >  bool validate(int slen, int sl, int sr, int alnpid, int adist) {
681     int alnlen=sr-sl+1;
682 +   if (alnpid>95) {
683 +     if (alnlen>=slen-2 || alnlen>21 ) return true;
684 +     }
685     sl--;sr--; //boundary is 0-based
686     int badj=0; //default boundary is 3 bases distance to end
687     int admax=1;

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