Package org.snpeff.coverage
Class CountFragments
java.lang.Object
org.snpeff.coverage.CountFragments
- All Implemented Interfaces:
Serializable
Base by base coverage (one chromsome)
- Author:
- pcingola
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)static CountFragments
calculateFromSam
(String samFile, boolean verbose) Calculate coverage from a SAM filevoid
Create new chromosome coveragevoid
Increment a regiontoString()
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Constructor Details
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CountFragments
public CountFragments()
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Method Details
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calculateFromSam
Calculate coverage from a SAM file- Parameters:
samFile
-verbose
-- Returns:
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avgCoverage
Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)- Parameters:
m
- : A marker interval- Returns:
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createChr
Create new chromosome coverage- Parameters:
chr
-len
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get
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inc
Increment a region- Parameters:
start
-end
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toString
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