htsjdk.samtools.util

Interface ReferenceSequenceMask

All Known Implementing Classes:

IntervalListReferenceSequenceMask, WholeGenomeReferenceSequenceMask

public interface ReferenceSequenceMask

Interface for specifying loci of interest for genotype calling and other operations. It is a requirement that the sequences be probed in ascending order.

Method Summary

Modifier and Type	Method and Description
boolean	get(int sequenceIndex, int position) It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
int	getMaxPosition()
int	getMaxSequenceIndex()
int	nextPosition(int sequenceIndex, int position) It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

Method Detail

get

boolean get(int sequenceIndex,
            int position)

It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

Returns:

true if the mask is set for the given sequence and position

nextPosition

int nextPosition(int sequenceIndex,
                 int position)

It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

Returns:

the next pos on the given sequence >= position that is set, or -1 if there are no more set positions

getMaxSequenceIndex

int getMaxSequenceIndex()

Returns:

Largest sequence index for which there are set bits.

getMaxPosition

int getMaxPosition()

Returns:

the largest position on the last sequence index