Package org.snpeff.coverage
Class CountReads
java.lang.Object
org.snpeff.coverage.CountReads
Count how many reads map (from many SAM/BAM files) onto markers
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addMarkerType
(Marker marker, String type) void
count()
Count markers from a fileint
int
int
Average read lengthint
long
void
setMarkerTypes
(MarkerTypes markerTypes) void
setVerbose
(boolean verbose)
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Field Details
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SHOW_EVERY
public static int SHOW_EVERY
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Constructor Details
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CountReads
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Method Details
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addMarkerType
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count
public void count()Count markers from a file -
getCountBases
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getCountExceptions
public int getCountExceptions() -
getCountReads
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getCountTotalReads
public int getCountTotalReads() -
getCountTypes
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getCoverageByExons
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getCoverageByType
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getMarkerTypes
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getReadLengthAvg
public int getReadLengthAvg()Average read length- Returns:
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getReadLengthCount
public int getReadLengthCount() -
getReadLengthSum
public long getReadLengthSum() -
setMarkerTypes
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setVerbose
public void setVerbose(boolean verbose)
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