org.utgenome.gwt.utgb.client.bio
Class SAMReadLight

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.Interval
      org.utgenome.gwt.utgb.client.bio.SAMReadLight

All Implemented Interfaces:

Serializable, Comparable<Interval>, GenomeRange

Direct Known Subclasses:

SAMRead

public class SAMReadLight
extends Interval

Light weight SAMRead

Author:

leo

See Also:

Serialized Form

Field Summary

String	cigar
int	flag
int	iSize
String	qname
int	unclippedEnd
int	unclippedStart

Constructor Summary

SAMReadLight()

SAMReadLight(int start, int end)

Method Summary

void	accept(GenomeRangeVisitor visitor)
String	getName()
String	getQV()
String	getSequence()
boolean	isAntiSense()
boolean	isFirstRead()
boolean	isMappedInProperPair()
boolean	isMate(SAMReadLight other)
boolean	isPairedRead()
boolean	isSecondRead()
boolean	isSense()
boolean	isUnmapped()
String	toString()
boolean	unclippedSequenceContains(int startOnGenome)
boolean	unclippedSequenceHasOverlapWith(SAMReadLight other)

Methods inherited from class org.utgenome.gwt.utgb.client.bio.Interval

adjustToOneOrigin, atomicSetStartAndEnd, compareTo, contains, contains, correctInterval, follows, getColor, getEnd, getStart, hasOverlap, intersect, intersectsWith, length, precedes, setEnd, setStart, toJSONArray

Methods inherited from class java.lang.Object

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

Field Detail

qname

public String qname

flag

public int flag

unclippedStart

public int unclippedStart

unclippedEnd

public int unclippedEnd

cigar

public String cigar

iSize

public int iSize

Constructor Detail

SAMReadLight

public SAMReadLight()

SAMReadLight

public SAMReadLight(int start,
                    int end)

Method Detail

toString

public String toString()

Overrides:

toString in class Interval

isMate

public boolean isMate(SAMReadLight other)

getName

public String getName()

Specified by:

getName in interface GenomeRange

Overrides:

getName in class Interval

isSense

public boolean isSense()

Specified by:

isSense in interface GenomeRange

Overrides:

isSense in class Interval

isAntiSense

public boolean isAntiSense()

Specified by:

isAntiSense in interface GenomeRange

Overrides:

isAntiSense in class Interval

getSequence

public String getSequence()

getQV

public String getQV()

isPairedRead

public boolean isPairedRead()

isMappedInProperPair

public boolean isMappedInProperPair()

isFirstRead

public boolean isFirstRead()

isSecondRead

public boolean isSecondRead()

isUnmapped

public boolean isUnmapped()

unclippedSequenceHasOverlapWith

public boolean unclippedSequenceHasOverlapWith(SAMReadLight other)

unclippedSequenceContains

public boolean unclippedSequenceContains(int startOnGenome)

accept

public void accept(GenomeRangeVisitor visitor)

Specified by:

accept in interface GenomeRange

Overrides:

accept in class Interval