htsjdk.samtools.util

Class AbstractRecordAndOffset

java.lang.Object

htsjdk.samtools.util.AbstractRecordAndOffset

Direct Known Subclasses:

EdgingRecordAndOffset, SamLocusIterator.RecordAndOffset

public class AbstractRecordAndOffset
extends java.lang.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 for SamLocusIterator.RecordAndOffset implementation or one alignment block of SAMRecord for TypedRecordAndOffset implementation.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AbstractRecordAndOffset.AlignmentType Classifies whether the given event is a match, insertion, or deletion.

Field Summary

Fields

Modifier and Type	Field and Description
protected AbstractRecordAndOffset.AlignmentType	alignmentType The AbstractRecordAndOffset.AlignmentType of this object, which classifies whether the given event is a match, insertion, or deletion when queried from a SamLocusIterator.
protected int	offset Zero-based offset in the read corresponding to the current position in AbstractLocusInfo
protected SAMRecord	record A SAMRecord aligned to reference position

Constructor Summary

Constructors

Constructor and Description
AbstractRecordAndOffset(SAMRecord record, int offset)
AbstractRecordAndOffset(SAMRecord record, int offset, AbstractRecordAndOffset.AlignmentType alignmentType)

Method Summary

Modifier and Type	Method and Description
AbstractRecordAndOffset.AlignmentType	getAlignmentType() The AbstractRecordAndOffset.AlignmentType of this object, which classifies whether the given event is a match, insertion, or deletion when queried from a SamLocusIterator.
byte[]	getBaseQualities()
byte	getBaseQuality()
int	getLength()
int	getOffset()
byte	getReadBase()
java.lang.String	getReadName()
SAMRecord	getRecord()
protected void	validateOffset(int offset, byte[] array)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

record

protected final SAMRecord record

A SAMRecord aligned to reference position

offset

protected final int offset

Zero-based offset in the read corresponding to the current position in AbstractLocusInfo

alignmentType

protected final AbstractRecordAndOffset.AlignmentType alignmentType

The AbstractRecordAndOffset.AlignmentType of this object, which classifies whether the given event is a match, insertion, or deletion when queried from a SamLocusIterator.

Constructor Detail

AbstractRecordAndOffset

public AbstractRecordAndOffset(SAMRecord record,
                               int offset)

Parameters:

record - inner SAMRecord

offset - from the start of the read

AbstractRecordAndOffset

public AbstractRecordAndOffset(SAMRecord record,
                               int offset,
                               AbstractRecordAndOffset.AlignmentType alignmentType)

Parameters:

record - inner SAMRecord

offset - from the start of the read

alignmentType - The AbstractRecordAndOffset.AlignmentType of this object, which is used when queried in a SamLocusIterator.

Method Detail

getOffset

public int getOffset()

Returns:

offset of aligned read base from the start of the read.

getRecord

public SAMRecord getRecord()

Returns:

inner SAMRecord object.

getAlignmentType

public AbstractRecordAndOffset.AlignmentType getAlignmentType()

The AbstractRecordAndOffset.AlignmentType of this object, which classifies whether the given event is a match, insertion, or deletion when queried from a SamLocusIterator.

getReadBase

public byte getReadBase()

Returns:

the read base according to offset.

getLength

public int getLength()

Returns:

the length of alignment block represented by the object.

getReadName

public java.lang.String getReadName()

Returns:

read name of inner SAMRecord.

getBaseQualities

public byte[] getBaseQualities()

Returns:

array of base qualities of inner SAMRecord.

getBaseQuality

public byte getBaseQuality()

Returns:

the base quality according to offset.

validateOffset

protected void validateOffset(int offset,
                              byte[] array)