Package org.snpeff.outputFormatter
Class BedOutputFormatter
- java.lang.Object
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- org.snpeff.outputFormatter.OutputFormatter
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- org.snpeff.outputFormatter.BedOutputFormatter
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- Direct Known Subclasses:
BedAnnotationOutputFormatter
public class BedOutputFormatter extends OutputFormatter
Formats output as BED file Referneces: http://genome.ucsc.edu/FAQ/FAQformat.html#format1- Author:
- pcingola
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Constructor Summary
Constructors Constructor Description BedOutputFormatter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
endSection(Marker marker)
Finish up sectionvoid
setOutOffset(int outOffset)
void
startSection(Marker marker)
Starts a new sectionjava.lang.String
toString()
Show all effectsjava.lang.String
toStringHeader()
Show header-
Methods inherited from class org.snpeff.outputFormatter.OutputFormatter
add, clone, close, print, printSection, setChrStr, setCommandLineStr, setConfig, setOutputFile, setShowHeader, setSupressOutput, setUseGeneId, setUseHgvs, setUseOicr, setUseSequenceOntology, setVariantEffectResutFilter, setVersion
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Method Detail
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endSection
public java.lang.String endSection(Marker marker)
Finish up section- Overrides:
endSection
in classOutputFormatter
- Parameters:
marker
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setOutOffset
public void setOutOffset(int outOffset)
- Overrides:
setOutOffset
in classOutputFormatter
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startSection
public void startSection(Marker marker)
Description copied from class:OutputFormatter
Starts a new section- Overrides:
startSection
in classOutputFormatter
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toString
public java.lang.String toString()
Show all effects- Overrides:
toString
in classOutputFormatter
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toStringHeader
public java.lang.String toStringHeader()
Show header- Specified by:
toStringHeader
in classOutputFormatter
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