Searched refs:getBaseQualitiesNoCopy (Results 1 – 9 of 9) sorted by relevance
340 final byte[] quals = getBaseQualitiesNoCopy();362 final byte[] quals = getBaseQualitiesNoCopy();411 default byte[] getBaseQualitiesNoCopy() { in getBaseQualitiesNoCopy() method
295 public byte[] getBaseQualitiesNoCopy() { in getBaseQualitiesNoCopy() method in SAMRecordToGATKReadAdapter
254 final byte[] baseQualities = read.getBaseQualitiesNoCopy(); in getBasesAndBaseQualitiesAlignedOneToOne()
255 final byte[] thisQuals = enclosingRead.getBaseQualitiesNoCopy(); in equalQualities()265 final byte[] otherQuals = other.enclosingRead.getBaseQualitiesNoCopy(); in equalQualities()266 final byte[] thisQuals = enclosingRead.getBaseQualitiesNoCopy(); in equalQualities()
339 …final byte[] quals = Arrays.copyOfRange(read.getBaseQualitiesNoCopy(), (int) (search >> 32), ((int… in insertAt()364 … Arrays.copyOfRange(read.getBaseQualitiesNoCopy(), readOffset, readOffset + len))); in inserts()372 … Arrays.copyOfRange(read.getBaseQualitiesNoCopy(), readOffset, readOffset + len))); in inserts()
85 final byte[] quals = read.getBaseQualitiesNoCopy(); in correctReads()
335 … HaplotypeCallerGenotypingDebugger.println(Arrays.toString(read.getBaseQualitiesNoCopy()));
121 final byte[] readbaseQuals = read.getBaseQualitiesNoCopy(); in anonymizeRead()
1479 final byte[] readQuals = read.getBaseQualitiesNoCopy(); in ReadReport()1861 … return calculateShortFragmentTrim(read, calculateQualityTrim(read.getBaseQualitiesNoCopy())); in calculateTrim()