Package org.snpeff.coverage
Class CountFragments
- java.lang.Object
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- org.snpeff.coverage.CountFragments
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- All Implemented Interfaces:
java.io.Serializable
public class CountFragments extends java.lang.Object implements java.io.Serializable
Base by base coverage (one chromsome)- Author:
- pcingola
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description CountFragments()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description double
avgCoverage(Marker m)
Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)static CountFragments
calculateFromSam(java.lang.String samFile, boolean verbose)
Calculate coverage from a SAM filevoid
createChr(java.lang.String chr, int len)
Create new chromosome coverageCoverageChr
get(java.lang.String chr)
void
inc(java.lang.String chr, int start, int end)
Increment a regionjava.lang.String
toString()
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Method Detail
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calculateFromSam
public static CountFragments calculateFromSam(java.lang.String samFile, boolean verbose)
Calculate coverage from a SAM file- Parameters:
samFile
-verbose
-- Returns:
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avgCoverage
public double avgCoverage(Marker m)
Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)- Parameters:
m
- : A marker interval- Returns:
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createChr
public void createChr(java.lang.String chr, int len)
Create new chromosome coverage- Parameters:
chr
-len
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get
public CoverageChr get(java.lang.String chr)
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inc
public void inc(java.lang.String chr, int start, int end)
Increment a region- Parameters:
start
-end
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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