uk.ac.sanger.npg.picard
Class AlignmentFilterMetric

java.lang.Object
  uk.ac.sanger.npg.picard.AlignmentFilterMetric

public class AlignmentFilterMetric
extends java.lang.Object

Nested Class Summary

static class

AlignmentFilterMetric.SQ SQ record in SAM header

Constructor Summary

AlignmentFilterMetric(int numberAlignments)

Method Summary

void	addRef(java.util.ArrayList<AlignmentFilterMetric.SQ> refSQList)
void	addRef(net.sf.samtools.SAMSequenceDictionary sequenceDictionary)
void	checkNextReadsForChimera(java.util.List<net.sf.samtools.SAMRecord> recordList, java.util.List<net.sf.samtools.SAMRecord> pairedRecordList)
int[][]	getChimericReadsCount()
int	getNumberAlignments()
int[]	getReadsCountByAlignedNumForward()
int[]	getReadsCountByAlignedNumReverse()
int[]	getReadsCountPerRef()
int	getReadsCountUnaligned()
java.util.ArrayList<java.util.ArrayList<AlignmentFilterMetric.SQ>>	getRefList()
int	getTotalReads()
void	output() log information
void	output(java.io.File outJson)
void	setChimericReadsCount(int[][] chimericReadsCount)
void	setNumberAlignments(int numberAlignments)
void	setReadsCountByAlignedNumForward(int[] readsCountByAlignedNum)
void	setReadsCountByAlignedNumReverse(int[] readsCountByAlignedNumReverse)
void	setReadsCountPerRef(int[] readsCountPerRef)
void	setReadsCountUnaligned(int readsCountUnaligned)
void	setRefList(java.util.ArrayList<java.util.ArrayList<AlignmentFilterMetric.SQ>> refList)
void	setTotalReads(int totalReads)

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentFilterMetric

public AlignmentFilterMetric(int numberAlignments)

Parameters:

numberAlignments -

Method Detail

checkNextReadsForChimera

public void checkNextReadsForChimera(java.util.List<net.sf.samtools.SAMRecord> recordList,
                                     java.util.List<net.sf.samtools.SAMRecord> pairedRecordList)

Parameters:

recordList -

pairedRecordList -

output

public void output()

log information

output

public void output(java.io.File outJson)

Parameters:

outJson -

getTotalReads

public int getTotalReads()

Returns:

the totalReads

setTotalReads

public void setTotalReads(int totalReads)

Parameters:

totalReads - the totalReads to set

getReadsCountPerRef

public int[] getReadsCountPerRef()

Returns:

the readsCountPerRef

setReadsCountPerRef

public void setReadsCountPerRef(int[] readsCountPerRef)

Parameters:

readsCountPerRef - the readsCountPerRef to set

getReadsCountUnaligned

public int getReadsCountUnaligned()

Returns:

the readsCountUnaligned

setReadsCountUnaligned

public void setReadsCountUnaligned(int readsCountUnaligned)

Parameters:

readsCountUnaligned - the readsCountUnaligned to set

getChimericReadsCount

public int[][] getChimericReadsCount()

Returns:

the chimericReadsCount

setChimericReadsCount

public void setChimericReadsCount(int[][] chimericReadsCount)

Parameters:

chimericReadsCount - the chimericReadsCount to set

getReadsCountByAlignedNumForward

public int[] getReadsCountByAlignedNumForward()

Returns:

the readsCountByAlignedNum

setReadsCountByAlignedNumForward

public void setReadsCountByAlignedNumForward(int[] readsCountByAlignedNum)

Parameters:

readsCountByAlignedNum - the readsCountByAlignedNum to set

getReadsCountByAlignedNumReverse

public int[] getReadsCountByAlignedNumReverse()

Returns:

the readsCountByAlignedNumReverse

setReadsCountByAlignedNumReverse

public void setReadsCountByAlignedNumReverse(int[] readsCountByAlignedNumReverse)

Parameters:

readsCountByAlignedNumReverse - the readsCountByAlignedNumReverse to set

getNumberAlignments

public int getNumberAlignments()

Returns:

the numberAlignments

setNumberAlignments

public void setNumberAlignments(int numberAlignments)

Parameters:

numberAlignments - the numberAlignments to set

addRef

public void addRef(net.sf.samtools.SAMSequenceDictionary sequenceDictionary)

addRef

public void addRef(java.util.ArrayList<AlignmentFilterMetric.SQ> refSQList)

Parameters:

refSQList -

getRefList

public java.util.ArrayList<java.util.ArrayList<AlignmentFilterMetric.SQ>> getRefList()

Returns:

the refList

setRefList

public void setRefList(java.util.ArrayList<java.util.ArrayList<AlignmentFilterMetric.SQ>> refList)

Parameters:

refList - the refList to set