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.

Field Summary

Fields

Modifier and Type	Field and Description
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, int length, int refPos)

Method Summary

Modifier and Type	Method and Description
byte[]	getBaseQualities()
byte	getBaseQuality()
int	getLength()
int	getOffset()
byte	getReadBase()
java.lang.String	getReadName()
SAMRecord	getRecord()
int	getRefPos()
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

Constructor Detail

AbstractRecordAndOffset

public AbstractRecordAndOffset(SAMRecord record,
                               int offset,
                               int length,
                               int refPos)

Parameters:

record - inner SAMRecord

offset - from the start of the read

length - of alignment block

refPos - corresponding to read offset reference position

AbstractRecordAndOffset

public AbstractRecordAndOffset(SAMRecord record,
                               int offset)

Parameters:

record - inner SAMRecord

offset - from the start of the read

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.

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.

getRefPos

public int getRefPos()

Returns:

the position in reference sequence, to which the start of alignment block is aligned.

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)