Package org.snpeff.outputFormatter
Class BedOutputFormatter
java.lang.Object
org.snpeff.outputFormatter.OutputFormatter
org.snpeff.outputFormatter.BedOutputFormatter
- Direct Known Subclasses:
BedAnnotationOutputFormatter
Formats output as BED file
Referneces: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
- Author:
- pcingola
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionendSection
(Marker marker) Finish up sectionvoid
setOutOffset
(int outOffset) void
startSection
(Marker marker) Starts a new sectiontoString()
Show all effectsShow headerMethods 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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Constructor Details
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BedOutputFormatter
public BedOutputFormatter()
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Method Details
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endSection
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
Description copied from class:OutputFormatter
Starts a new section- Overrides:
startSection
in classOutputFormatter
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toString
Show all effects- Overrides:
toString
in classOutputFormatter
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toStringHeader
Show header- Specified by:
toStringHeader
in classOutputFormatter
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