Package org.snpeff.snpEffect
Interface VcfAnnotator
- All Superinterfaces:
CommandLine
- All Known Implementing Classes:
SnpEffCmdEff
,VcfAnnotatorChain
Annotate a VCF file: E.g. add information to INFO column
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Method Summary
Modifier and TypeMethodDescriptionboolean
addHeaders
(VcfFileIterator vcfFile) Add annotation headers to VCF fileboolean
Annotate a VCF file entryboolean
annotateFinish
(VcfFileIterator vcfFile) This method is called after all annotations have been performed.boolean
annotateInit
(VcfFileIterator vcfFile) Initialize annotator: This method is called after vcfFile is opened, but before the header is output.void
Set configurationvoid
setDebug
(boolean debug) Set debug modevoid
setVerbose
(boolean verbose) Set verbose modeMethods inherited from interface org.snpeff.snpEffect.commandLine.CommandLine
getArgs, parseArgs, run, usage
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Method Details
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addHeaders
Add annotation headers to VCF file- Returns:
- true if OK, false on error
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annotate
Annotate a VCF file entry- Returns:
- true if the entry was annotated
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annotateFinish
This method is called after all annotations have been performed. The vcfFile might have already been closed by this time (i.e. the VcfFileIterator reached the end).- Returns:
- true if OK, false on error
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annotateInit
Initialize annotator: This method is called after vcfFile is opened, but before the header is output. The first vcfEntry might have (and often has) already been read from the file.- Returns:
- true if OK, false on error
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setConfig
Set configuration -
setDebug
void setDebug(boolean debug) Set debug mode -
setVerbose
void setVerbose(boolean verbose) Set verbose mode
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