Class VcfOutputFormatter
java.lang.Object
org.snpeff.outputFormatter.OutputFormatter
org.snpeff.outputFormatter.VcfOutputFormatter
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionVcfOutputFormatter(List<VcfEntry> vcfEntries) Add all vcf entries to a list (used only for debugging and test-cases) -
Method Summary
Modifier and TypeMethodDescriptionprotected voidAdd headerprotected voidAdd effects to INFO fieldclone()endSection(Marker marker) Finish up sectionNew lines to be added to headervoidsetFormatVersion(EffFormatVersion formatVersion) voidsetGatk(boolean gatk) voidsetLossOfFunction(boolean lossOfFunction) voidsetOutOffset(int outOffset) voidstartSection(Marker marker) Starts a new sectiontoString()protected StringShow headerMethods inherited from class OutputFormatter
add, close, print, printSection, setChrStr, setCommandLineStr, setConfig, setOutputFile, setShowHeader, setSupressOutput, setUseGeneId, setUseHgvs, setUseOicr, setUseSequenceOntology, setVariantEffectResutFilter, setVersion
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Field Details
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debug
public static boolean debug -
VCF_INFO_OICR_NAME
- See Also:
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Constructor Details
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VcfOutputFormatter
public VcfOutputFormatter() -
VcfOutputFormatter
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Method Details
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addHeader
protected void addHeader()Add header -
addInfo
Add effects to INFO field -
clone
- Overrides:
clonein classOutputFormatter
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endSection
Finish up section- Overrides:
endSectionin classOutputFormatter
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getNewHeaderLines
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setFormatVersion
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setGatk
public void setGatk(boolean gatk) -
setLossOfFunction
public void setLossOfFunction(boolean lossOfFunction) -
setOutOffset
public void setOutOffset(int outOffset) - Overrides:
setOutOffsetin classOutputFormatter
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startSection
Description copied from class:OutputFormatterStarts a new section- Overrides:
startSectionin classOutputFormatter
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toString
- Overrides:
toStringin classOutputFormatter
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toStringHeader
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