Package htsjdk.samtools.util
Class IntervalListReferenceSequenceMask
java.lang.Object
htsjdk.samtools.util.IntervalListReferenceSequenceMask
- All Implemented Interfaces:
ReferenceSequenceMask
Serve up loci of interest based on an interval list.
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Constructor Summary
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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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Constructor Details
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IntervalListReferenceSequenceMask
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Method Details
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get
public boolean get(int sequenceIndex, int position) It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.- Specified by:
get
in interfaceReferenceSequenceMask
- Returns:
- true if the mask is set for the given sequence and position
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nextPosition
public int nextPosition(int sequenceIndex, int position) It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.- Specified by:
nextPosition
in interfaceReferenceSequenceMask
- 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
public int getMaxSequenceIndex()- Specified by:
getMaxSequenceIndex
in interfaceReferenceSequenceMask
- Returns:
- Largest sequence index for which there are set bits.
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getMaxPosition
public int getMaxPosition()- Specified by:
getMaxPosition
in interfaceReferenceSequenceMask
- Returns:
- the largest position on the last sequence index
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getHeader
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