Package org.snpeff.coverage
Class CountReadsOnMarkers
- java.lang.Object
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- org.snpeff.coverage.CountReadsOnMarkers
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public class CountReadsOnMarkers 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 boolean
debug
static int
MAX_EXONS_CHART
static int
SHOW_EVERY
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Constructor Summary
Constructors Constructor Description CountReadsOnMarkers(SnpEffectPredictor snpEffectPredictor)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addFile(java.lang.String samFileName)
Add a SAM/BAM file to be processedvoid
addMarkerType(Marker marker, java.lang.String type)
void
count()
Count markers from all filesMarkerTypes
getMarkerTypes()
int
getReadLengthAvg()
Average read lengthjava.lang.String
html()
Show charts in htmljava.lang.String
probabilityTable(CountByType prob)
Show probabilitiesvoid
setVerbose(boolean verbose)
java.lang.String
toString()
Print table to STDOUT
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Field Detail
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SHOW_EVERY
public static final int SHOW_EVERY
- See Also:
- Constant Field Values
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MAX_EXONS_CHART
public static final int MAX_EXONS_CHART
- See Also:
- Constant Field Values
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debug
public static boolean debug
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Constructor Detail
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CountReadsOnMarkers
public CountReadsOnMarkers(SnpEffectPredictor snpEffectPredictor)
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Method Detail
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addFile
public void addFile(java.lang.String samFileName)
Add a SAM/BAM file to be processed- Parameters:
samFileName
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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 all files
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getMarkerTypes
public MarkerTypes getMarkerTypes()
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getReadLengthAvg
public int getReadLengthAvg()
Average read length- Returns:
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html
public java.lang.String html()
Show charts in html- Returns:
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probabilityTable
public java.lang.String probabilityTable(CountByType prob)
Show probabilities- Parameters:
prob
- : Probabilities for each- Returns:
- A string showing a tab delimited table
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setVerbose
public void setVerbose(boolean verbose)
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toString
public java.lang.String toString()
Print table to STDOUT- Overrides:
toString
in classjava.lang.Object
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