Package htsjdk.samtools.util
Interface ReferenceSequenceMask
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- 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.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method 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.
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Method Detail
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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
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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
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getMaxSequenceIndex
int getMaxSequenceIndex()
- Returns:
- Largest sequence index for which there are set bits.
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getMaxPosition
int getMaxPosition()
- Returns:
- the largest position on the last sequence index
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