Package htsjdk.samtools.util

Class EdgingRecordAndOffset

java.lang.Object

htsjdk.samtools.util.AbstractRecordAndOffset

htsjdk.samtools.util.EdgingRecordAndOffset

public abstract class EdgingRecordAndOffset
extends AbstractRecordAndOffset

Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds to the base and quality for the start of alignment block at the genomic position described by the AbstractLocusInfo. This is implementation for EdgeReadIterator, field type added to indicate whether object represents the start or the end of an alignment block.

Subclasses StartEdgingRecordAndOffset and EndEdgingRecordAndOffset are used in EdgeReadIterator to distinguish starting and ending of the alignment block as for each alignment block two objects of EdgingRecordAndOffset are created with two different types. The main idea of using EdgeReadIterator is to process alignment block starting from locus where BEGIN type occurs, aggregate information per locus and keep it until END type occurs, then remove alignment block from consideration.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	EdgingRecordAndOffset.Type	Describes the type of TypedRecordAndOffset, whether it represents the start or the end of an alignment block.

Nested classes/interfaces inherited from class htsjdk.samtools.util.AbstractRecordAndOffset

AbstractRecordAndOffset.AlignmentType

Field Summary

Fields inherited from class htsjdk.samtools.util.AbstractRecordAndOffset

alignmentType, offset, record

Method Summary

Modifier and Type	Method	Description
static EdgingRecordAndOffset	createBeginRecord(SAMRecord record, int offset, int length, int refPos)
static EdgingRecordAndOffset	createEndRecord(EdgingRecordAndOffset startRecord)
abstract byte	getBaseQuality(int position)
abstract int	getRefPos()
abstract EdgingRecordAndOffset	getStart()
abstract EdgingRecordAndOffset.Type	getType()

Methods inherited from class htsjdk.samtools.util.AbstractRecordAndOffset

getAlignmentType, getBaseQualities, getBaseQuality, getLength, getOffset, getReadBase, getReadName, getRecord, validateOffset

Methods inherited from class java.lang.Object

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

Method Details

getStart

public abstract EdgingRecordAndOffset getStart()

getType

public abstract EdgingRecordAndOffset.Type getType()

getBaseQuality

public abstract byte getBaseQuality(int position)

getRefPos

public abstract int getRefPos()

createBeginRecord

public static EdgingRecordAndOffset createBeginRecord(SAMRecord record,
 int offset,
 int length,
 int refPos)

createEndRecord

public static EdgingRecordAndOffset createEndRecord(EdgingRecordAndOffset startRecord)