Searched refs:offsetAndOperator (Results 1 – 2 of 2) sorted by relevance
47 …final Pair<Integer, CigarOperator> offsetAndOperator = ReadUtils.getReadIndexForReferenceCoordinat… in adjustQualsOfOverlappingPairedFragments() local48 final CigarOperator operator = offsetAndOperator.getRight(); in adjustQualsOfOverlappingPairedFragments()49 final int offset = offsetAndOperator.getLeft(); in adjustQualsOfOverlappingPairedFragments()
720 …final Pair<Integer, CigarOperator> offsetAndOperator = getReadIndexForReferenceCoordinate(read, re… in getReadBaseAtReferenceCoordinate() local721 …return (offsetAndOperator.getLeft() != READ_INDEX_NOT_FOUND && offsetAndOperator.getRight().consum… in getReadBaseAtReferenceCoordinate()722 Optional.of(read.getBase(offsetAndOperator.getLeft())) : Optional.empty(); in getReadBaseAtReferenceCoordinate()729 …final Pair<Integer, CigarOperator> offsetAndOperator = getReadIndexForReferenceCoordinate(read.get… in getReadBaseQualityAtReferenceCoordinate() local730 …return (offsetAndOperator.getRight() != null && offsetAndOperator.getRight().consumesReadBases()) ? in getReadBaseQualityAtReferenceCoordinate()731 Optional.of(read.getBaseQuality(offsetAndOperator.getLeft())) : Optional.empty(); in getReadBaseQualityAtReferenceCoordinate()