Lines Matching refs:ali_it1
331 …g & cigar, TString & mutations, TIter ali_it0, TIter ali_it0_stop, TIter ali_it1, TIter ali_it1_st… in getCigarLine() argument
346 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
351 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
354 if(*ali_it1 != *ali_it0) in getCigarLine()
362 ++ali_it1; in getCigarLine()
369 ++ali_it1; in getCigarLine()
373 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
376 ++ali_it1; in getCigarLine()
393 while(ali_it1 != ali_it1_stop) in getCigarLine()
395 ++ali_it1; in getCigarLine()
412 TIter ali_it0, TIter ali_it0_stop, TIter ali_it1, TIter ali_it1_stop) in getCigarLine() argument
426 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
431 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
434 if(*ali_it1 != *ali_it0) in getCigarLine()
438 ++ali_it1; in getCigarLine()
445 ++ali_it1; in getCigarLine()
449 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
452 ++ali_it1; in getCigarLine()
467 while(ali_it1 != ali_it1_stop) in getCigarLine()
469 ++ali_it1; in getCigarLine()
1315 TAlignIterator ali_it1 = iter(row(align,1),viewPosReadFirst); in dumpMatches() local
1319 getCigarLine(align,cigar,mutations,ali_it0,ali_it0stop,ali_it1,ali_it1stop); in dumpMatches()