org.utgenome.core.cui
Class ReadStat.ReadAlignmentStat

java.lang.Object
  org.utgenome.core.cui.ReadStat.ReadAlignmentStat

Enclosing class:

ReadStat

public static class ReadStat.ReadAlignmentStat
extends Object

Field Summary

List<String>	bamFile
long	numAlignedWithSW
long	numBothEndIsMapped
long	numBothEndIsUnmapped
long	numMapped
long	numOneEndIsMapped
long	numPairs
long	numRead
long	numRepeat
long	numUnique
long	numUnmapped

Constructor Summary

ReadStat.ReadAlignmentStat()

ReadStat.ReadAlignmentStat(String bamFile)

Method Summary

void	add(ReadStat.ReadAlignmentStat other)
String	getMappedRate()
String	getRepeatMappedRate()
String	getUniquelyMapppedRate()

Methods inherited from class java.lang.Object

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

Field Detail

bamFile

public List<String> bamFile

numRead

public long numRead

numMapped

public long numMapped

numUnmapped

public long numUnmapped

numUnique

public long numUnique

numRepeat

public long numRepeat

numAlignedWithSW

public long numAlignedWithSW

numPairs

public long numPairs

numBothEndIsMapped

public long numBothEndIsMapped

numOneEndIsMapped

public long numOneEndIsMapped

numBothEndIsUnmapped

public long numBothEndIsUnmapped

Constructor Detail

ReadStat.ReadAlignmentStat

public ReadStat.ReadAlignmentStat()

ReadStat.ReadAlignmentStat

public ReadStat.ReadAlignmentStat(String bamFile)

Method Detail

getMappedRate

public String getMappedRate()

getUniquelyMapppedRate

public String getUniquelyMapppedRate()

getRepeatMappedRate

public String getRepeatMappedRate()

add

public void add(ReadStat.ReadAlignmentStat other)