Package org.snpeff.coverage
Class CountReads
- java.lang.Object
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- org.snpeff.coverage.CountReads
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public class CountReads extends java.lang.Object
Count how many reads map (from many SAM/BAM files) onto markers- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static int
SHOW_EVERY
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Constructor Summary
Constructors Constructor Description CountReads(java.lang.String fileName, SnpEffectPredictor snpEffectPredictor)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addMarkerType(Marker marker, java.lang.String type)
void
count()
Count markers from a fileCountByKey<Marker>
getCountBases()
int
getCountExceptions()
CountByKey<Marker>
getCountReads()
int
getCountTotalReads()
CountByType
getCountTypes()
java.util.ArrayList<CoverageByType>
getCoverageByExons()
CoverageByType
getCoverageByType()
MarkerTypes
getMarkerTypes()
int
getReadLengthAvg()
Average read lengthint
getReadLengthCount()
long
getReadLengthSum()
void
setMarkerTypes(MarkerTypes markerTypes)
void
setVerbose(boolean verbose)
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Constructor Detail
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CountReads
public CountReads(java.lang.String fileName, SnpEffectPredictor snpEffectPredictor)
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Method Detail
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addMarkerType
public void addMarkerType(Marker marker, java.lang.String type)
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count
public void count()
Count markers from a file
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getCountBases
public CountByKey<Marker> getCountBases()
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getCountExceptions
public int getCountExceptions()
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getCountReads
public CountByKey<Marker> getCountReads()
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getCountTotalReads
public int getCountTotalReads()
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getCountTypes
public CountByType getCountTypes()
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getCoverageByExons
public java.util.ArrayList<CoverageByType> getCoverageByExons()
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getCoverageByType
public CoverageByType getCoverageByType()
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getMarkerTypes
public MarkerTypes getMarkerTypes()
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getReadLengthAvg
public int getReadLengthAvg()
Average read length- Returns:
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getReadLengthCount
public int getReadLengthCount()
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getReadLengthSum
public long getReadLengthSum()
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setMarkerTypes
public void setMarkerTypes(MarkerTypes markerTypes)
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setVerbose
public void setVerbose(boolean verbose)
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