Package org.snpeff.outputFormatter
Class VcfOutputFormatter
java.lang.Object
org.snpeff.outputFormatter.OutputFormatter
org.snpeff.outputFormatter.VcfOutputFormatter
Formats output as VCF
- Author:
- pcingola
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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 void
Add headerprotected void
Add effects to INFO fieldclone()
endSection
(Marker marker) Finish up sectionNew lines to be added to headervoid
setFormatVersion
(EffFormatVersion formatVersion) void
setGatk
(boolean gatk) void
setLossOfFunction
(boolean lossOfFunction) void
setOutOffset
(int outOffset) void
startSection
(Marker marker) Starts a new sectiontoString()
protected String
Show headerMethods inherited from class org.snpeff.outputFormatter.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
Add all vcf entries to a list (used only for debugging and test-cases)
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Method Details
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addHeader
protected void addHeader()Add header -
addInfo
Add effects to INFO field -
clone
- Overrides:
clone
in classOutputFormatter
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endSection
Finish up section- Overrides:
endSection
in classOutputFormatter
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getNewHeaderLines
New lines to be added to header -
setFormatVersion
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setGatk
public void setGatk(boolean gatk) -
setLossOfFunction
public void setLossOfFunction(boolean lossOfFunction) -
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
- Overrides:
toString
in classOutputFormatter
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toStringHeader
Show header- Specified by:
toStringHeader
in classOutputFormatter
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