org.broadinstitute.hellbender.utils.bwa

Class BwaMemAlignment

java.lang.Object

org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

public class BwaMemAlignment
extends java.lang.Object

Info from the Aligner about an alignment to reference that it discovered for some sequence. Please note that the refId is with respect to the BWA index reference names. These won't necessarily agree with reference IDs in SAM or BAM headers.

Constructor Summary

Constructors

Constructor and Description
BwaMemAlignment(int samFlag, int refId, int refStart, int refEnd, int seqStart, int seqEnd, int mapQual, int nMismatches, int alignerScore, int suboptimalScore, java.lang.String cigar, java.lang.String mdTag, java.lang.String xaTag, int mateRefId, int mateRefStart, int templateLen)

Method Summary

Modifier and Type	Method and Description
int	getAlignerScore()
java.lang.String	getCigar()
int	getMapQual()
int	getMateRefId()
int	getMateRefStart()
java.lang.String	getMDTag()
int	getNMismatches()
int	getRefEnd()
int	getRefId()
int	getRefStart()
int	getSamFlag()
int	getSeqEnd()
int	getSeqStart()
int	getSuboptimalScore()
int	getTemplateLen()
java.lang.String	getXATag()

Methods inherited from class java.lang.Object

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

Constructor Detail

BwaMemAlignment

public BwaMemAlignment(int samFlag,
                       int refId,
                       int refStart,
                       int refEnd,
                       int seqStart,
                       int seqEnd,
                       int mapQual,
                       int nMismatches,
                       int alignerScore,
                       int suboptimalScore,
                       java.lang.String cigar,
                       java.lang.String mdTag,
                       java.lang.String xaTag,
                       int mateRefId,
                       int mateRefStart,
                       int templateLen)

Method Detail

getSamFlag

public int getSamFlag()

getRefId

public int getRefId()

getRefStart

public int getRefStart()

getRefEnd

public int getRefEnd()

getSeqStart

public int getSeqStart()

getSeqEnd

public int getSeqEnd()

getMapQual

public int getMapQual()

getNMismatches

public int getNMismatches()

getAlignerScore

public int getAlignerScore()

getSuboptimalScore

public int getSuboptimalScore()

getCigar

public java.lang.String getCigar()

getMDTag

public java.lang.String getMDTag()

getXATag

public java.lang.String getXATag()

getMateRefId

public int getMateRefId()

getMateRefStart

public int getMateRefStart()

getTemplateLen

public int getTemplateLen()