Package org.snpeff.coverage
Class CountReadsOnMarkers
java.lang.Object
org.snpeff.coverage.CountReadsOnMarkers
Count how many reads map (from many SAM/BAM files) onto markers
- Author:
- pcingola
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic boolean
static final int
static final int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add a SAM/BAM file to be processedvoid
addMarkerType
(Marker marker, String type) void
count()
Count markers from all filesint
Average read lengthhtml()
Show charts in htmlprobabilityTable
(CountByType prob) Show probabilitiesvoid
setVerbose
(boolean verbose) toString()
Print table to STDOUT
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Field Details
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SHOW_EVERY
public static final int SHOW_EVERY- See Also:
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MAX_EXONS_CHART
public static final int MAX_EXONS_CHART- See Also:
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debug
public static boolean debug
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Constructor Details
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CountReadsOnMarkers
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Method Details
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addFile
Add a SAM/BAM file to be processed- Parameters:
samFileName
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addMarkerType
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count
public void count()Count markers from all files -
getMarkerTypes
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getReadLengthAvg
public int getReadLengthAvg()Average read length- Returns:
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html
Show charts in html- Returns:
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probabilityTable
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) -
toString
Print table to STDOUT
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