Package org.snpeff.outputFormatter
Class OutputFormatter
java.lang.Object
org.snpeff.outputFormatter.OutputFormatter
- Direct Known Subclasses:
BedOutputFormatter
,VcfOutputFormatter
Formats output
How is this used:
- newSection(); // Create a new 'section' on the output format (e.g. a new Marker)
- add(); // Add all changes related to this section (i.e. all changes related to this marker)
- endSection(); // Output all changes related to this section (output header if needed), clean up list of changes
- Author:
- pcingola
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
add
(VariantEffect variantEffect) Add effects to listclone()
void
close()
CLose output files, if anyendSection
(Marker marker) Finish up sectionvoid
Print a "raw" string to a filevoid
printSection
(Marker marker) End this section and print resultsvoid
void
setCommandLineStr
(String commandLineStr) void
void
setOutOffset
(int outOffset) void
setOutputFile
(String outputFile) void
setShowHeader
(boolean showHeader) void
setSupressOutput
(boolean supressOutput) void
setUseGeneId
(boolean useGeneId) void
setUseHgvs
(boolean useHgvs) void
setUseOicr
(boolean useOicr) void
setUseSequenceOntology
(boolean useSequenceOntology) void
setVariantEffectResutFilter
(VariantEffectFilter changeEffectResutFilter) void
setVersion
(String version) void
startSection
(Marker marker) Starts a new sectiontoString()
protected abstract String
Show header
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Constructor Details
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OutputFormatter
public OutputFormatter()
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Method Details
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add
Add effects to list -
clone
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close
public void close()CLose output files, if any -
endSection
Finish up section -
print
Print a "raw" string to a file -
printSection
End this section and print results -
setChrStr
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setCommandLineStr
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setConfig
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setOutOffset
public void setOutOffset(int outOffset) -
setOutputFile
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setShowHeader
public void setShowHeader(boolean showHeader) -
setSupressOutput
public void setSupressOutput(boolean supressOutput) -
setUseGeneId
public void setUseGeneId(boolean useGeneId) -
setUseHgvs
public void setUseHgvs(boolean useHgvs) -
setUseOicr
public void setUseOicr(boolean useOicr) -
setUseSequenceOntology
public void setUseSequenceOntology(boolean useSequenceOntology) -
setVariantEffectResutFilter
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setVersion
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startSection
Starts a new section -
toString
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toStringHeader
Show header
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