Searched refs:hasIndel (Results 1 – 11 of 11) sorted by relevance
444 bool hasIndel = false; in alignmentHasIndel() local445 for(unsigned i = 0; !hasIndel && i < length(rows(align)); ++i) in alignmentHasIndel()453 hasIndel = true; in alignmentHasIndel()459 return hasIndel; in alignmentHasIndel()735 bool hasIndel = false; in readMatchesFromGFF_Batch() local1021 hasIndel = true; in readMatchesFromGFF_Batch()1038 hasIndel = true; in readMatchesFromGFF_Batch()1113 if(splitRead && hasIndel) in readMatchesFromGFF_Batch()1116 if(!options.realign && splitRead && length(tmpCigarStr)<=3) hasIndel = false; in readMatchesFromGFF_Batch()1118 if(hasIndel) in readMatchesFromGFF_Batch()
329 unsigned hasIndel:1; // is 1 if read match contains indels, 0 else --> gaps
487 bool hasIndel();
398 bool Cigar::hasIndel() in hasIndel() function in Cigar
595 bool hasIndel = false; in main() local598 hasIndel = true; in main()602 if (!hasIndel) { in main()
569 bool hasIndel = false; in main() local572 hasIndel = true; in main()576 if (!hasIndel) { in main()
391 unsigned hasIndel:1; // is 1 if read match contains indels, 0 else --> gaps567 bool hasIndel = false;620 hasIndel = true;743 if(!options.realign && length(record.cigar)<=3) hasIndel = false;744 if(hasIndel)
335 bool hasIndel = false; in alignmentHasIndel() local336 for(unsigned i = 0; !hasIndel && i < length(rows(align)); ++i) in alignmentHasIndel()344 hasIndel = true; in alignmentHasIndel()350 return hasIndel; in alignmentHasIndel()
336 bool hasIndel = false; in alignmentHasIndel() local337 for(unsigned i = 0; !hasIndel && i < length(rows(align)); ++i) in alignmentHasIndel()345 hasIndel = true; in alignmentHasIndel()351 return hasIndel; in alignmentHasIndel()
696 bool hasIndel = false;1032 hasIndel = true;1051 hasIndel = true;1189 if(splitRead && hasIndel)1192 if(!options.realign && splitRead && length(tmpCigarStr)<=3) hasIndel = false;1194 if(hasIndel)1427 bool hasIndel = false;1513 hasIndel = true;1518 hasIndel = true;1686 if(splitRead && hasIndel)[all …]