Package 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.
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Method Summary
Modifier and TypeMethodDescriptionboolean
get
(int sequenceIndex, int position) It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.int
int
int
nextPosition
(int sequenceIndex, int position) It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
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Method Details
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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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