htsjdk.samtools.util

Class SamLocusIterator.RecordAndOffset

java.lang.Object

htsjdk.samtools.util.AbstractRecordAndOffset

htsjdk.samtools.util.SamLocusIterator.RecordAndOffset

Enclosing class:

SamLocusIterator

public static class SamLocusIterator.RecordAndOffset
extends AbstractRecordAndOffset

Implementation of AbstractRecordAndOffset class for SamLocusIterator. One object represents one aligned base of inner SAMRecord.

Nested Class Summary

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

Constructor Summary

Constructors

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

Method Summary

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

Constructor Detail

RecordAndOffset

public RecordAndOffset(SAMRecord record,
                       int offset)

Parameters:

record - inner SAMRecord

offset - 0-based offset from the start of SAMRecord

RecordAndOffset

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

Parameters:

record - inner SAMRecord

offset - 0-based offset from the start of SAMRecord

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