Searched refs:includeHardClip (Results 1 – 1 of 1) sorted by relevance
838 return calcCigarLength(cigar, includeSoftClip, includeHardClip); in calcCigarLength()865 if(includeHardClip){len+=current;} in calcCigarLength()900 if(includeHardClip){len+=current;} in calcCigarReadLength()930 if(includeHardClip){len+=current;} in calcCigarBases()954 if(includeHardClip){ in countLeadingClip()976 if(includeHardClip){len+=countTrailingHardClip(cigar);} in countTrailingClip()2002 public Read toRead(boolean parseCustom, boolean includeHardClip){ in toRead() argument2049 int start_=start(true, includeHardClip); in toRead()2050 int stop_=stop(start_, true, includeHardClip); in toRead()2457 public int start(boolean includeSoftClip, boolean includeHardClip){ in start() argument[all …]