Package htsjdk.samtools.util
Class AbstractRecordAndOffset
- java.lang.Object
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- htsjdk.samtools.util.AbstractRecordAndOffset
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- Direct Known Subclasses:
EdgingRecordAndOffset
,SamLocusIterator.RecordAndOffset
public class AbstractRecordAndOffset extends Object
Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds to the base and quality at the genomic position described the containing AbstractLocusInfo. One object represents one base forSamLocusIterator.RecordAndOffset
implementation or one alignment block ofSAMRecord
forTypedRecordAndOffset
implementation.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
AbstractRecordAndOffset.AlignmentType
Classifies whether the given event is a match, insertion, or deletion.
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Field Summary
Fields Modifier and Type Field Description protected AbstractRecordAndOffset.AlignmentType
alignmentType
TheAbstractRecordAndOffset.AlignmentType
of this object, which classifies whether the given event is a match, insertion, or deletion when queried from aSamLocusIterator
.protected int
offset
Zero-based offset in the read corresponding to the current position in AbstractLocusInfoprotected SAMRecord
record
A SAMRecord aligned to reference position
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Constructor Summary
Constructors Constructor Description AbstractRecordAndOffset(SAMRecord record, int offset)
AbstractRecordAndOffset(SAMRecord record, int offset, AbstractRecordAndOffset.AlignmentType alignmentType)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description AbstractRecordAndOffset.AlignmentType
getAlignmentType()
TheAbstractRecordAndOffset.AlignmentType
of this object, which classifies whether the given event is a match, insertion, or deletion when queried from aSamLocusIterator
.byte[]
getBaseQualities()
byte
getBaseQuality()
int
getLength()
int
getOffset()
byte
getReadBase()
String
getReadName()
SAMRecord
getRecord()
protected void
validateOffset(int offset, byte[] array)
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Field Detail
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record
protected final SAMRecord record
A SAMRecord aligned to reference position
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offset
protected final int offset
Zero-based offset in the read corresponding to the current position in AbstractLocusInfo
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alignmentType
protected final AbstractRecordAndOffset.AlignmentType alignmentType
TheAbstractRecordAndOffset.AlignmentType
of this object, which classifies whether the given event is a match, insertion, or deletion when queried from aSamLocusIterator
.
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Constructor Detail
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AbstractRecordAndOffset
public AbstractRecordAndOffset(SAMRecord record, int offset)
- Parameters:
record
- inner SAMRecordoffset
- from the start of the read
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AbstractRecordAndOffset
public AbstractRecordAndOffset(SAMRecord record, int offset, AbstractRecordAndOffset.AlignmentType alignmentType)
- Parameters:
record
- inner SAMRecordoffset
- from the start of the readalignmentType
- TheAbstractRecordAndOffset.AlignmentType
of this object, which is used when queried in aSamLocusIterator
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Method Detail
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getOffset
public int getOffset()
- Returns:
- offset of aligned read base from the start of the read.
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getRecord
public SAMRecord getRecord()
- Returns:
- inner
SAMRecord
object.
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getAlignmentType
public AbstractRecordAndOffset.AlignmentType getAlignmentType()
TheAbstractRecordAndOffset.AlignmentType
of this object, which classifies whether the given event is a match, insertion, or deletion when queried from aSamLocusIterator
.
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getReadBase
public byte getReadBase()
- Returns:
- the read base according to
offset
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getLength
public int getLength()
- Returns:
- the length of alignment block represented by the object.
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getReadName
public String getReadName()
- Returns:
- read name of inner SAMRecord.
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getBaseQualities
public byte[] getBaseQualities()
- Returns:
- array of base qualities of inner SAMRecord.
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getBaseQuality
public byte getBaseQuality()
- Returns:
- the base quality according to
offset
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validateOffset
protected void validateOffset(int offset, byte[] array)
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