Package htsjdk.samtools.util
Class IntervalListReferenceSequenceMask
- java.lang.Object
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- htsjdk.samtools.util.IntervalListReferenceSequenceMask
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- All Implemented Interfaces:
ReferenceSequenceMask
public class IntervalListReferenceSequenceMask extends Object implements ReferenceSequenceMask
Serve up loci of interest based on an interval list.
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Constructor Summary
Constructors Constructor Description IntervalListReferenceSequenceMask(IntervalList intervalList)
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Method Summary
All Methods Instance Methods Concrete 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.SAMFileHeader
getHeader()
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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Constructor Detail
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IntervalListReferenceSequenceMask
public IntervalListReferenceSequenceMask(IntervalList intervalList)
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Method Detail
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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
public SAMFileHeader getHeader()
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