Package org.snpeff.coverage

Class CountReads

java.lang.Object

org.snpeff.coverage.CountReads

public class CountReads
extends java.lang.Object

Count how many reads map (from many SAM/BAM files) onto markers

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static int	SHOW_EVERY

Constructor Summary

Constructors

Constructor	Description
CountReads(java.lang.String fileName, SnpEffectPredictor snpEffectPredictor)

Method Summary

Modifier and Type	Method	Description
void	addMarkerType(Marker marker, java.lang.String type)
void	count()	Count markers from a file
CountByKey<Marker>	getCountBases()
int	getCountExceptions()
CountByKey<Marker>	getCountReads()
int	getCountTotalReads()
CountByType	getCountTypes()
java.util.ArrayList<CoverageByType>	getCoverageByExons()
CoverageByType	getCoverageByType()
MarkerTypes	getMarkerTypes()
int	getReadLengthAvg()	Average read length
int	getReadLengthCount()
long	getReadLengthSum()
void	setMarkerTypes(MarkerTypes markerTypes)
void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

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

Field Detail

SHOW_EVERY

public static int SHOW_EVERY

Constructor Detail

CountReads

public CountReads(java.lang.String fileName,
                  SnpEffectPredictor snpEffectPredictor)

Method Detail

addMarkerType

public void addMarkerType(Marker marker,
                          java.lang.String type)

count

public void count()

Count markers from a file

getCountBases

public CountByKey<Marker> getCountBases()

getCountExceptions

public int getCountExceptions()

getCountReads

public CountByKey<Marker> getCountReads()

getCountTotalReads

public int getCountTotalReads()

getCountTypes

public CountByType getCountTypes()

getCoverageByExons

public java.util.ArrayList<CoverageByType> getCoverageByExons()

getCoverageByType

public CoverageByType getCoverageByType()

getMarkerTypes

public MarkerTypes getMarkerTypes()

getReadLengthAvg

public int getReadLengthAvg()

Average read length

Returns:

getReadLengthCount

public int getReadLengthCount()

getReadLengthSum

public long getReadLengthSum()

setMarkerTypes

public void setMarkerTypes(MarkerTypes markerTypes)

setVerbose

public void setVerbose(boolean verbose)