Package org.snpeff.snpEffect
Class VcfAnnotatorChain
- java.lang.Object
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- org.snpeff.snpEffect.VcfAnnotatorChain
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- All Implemented Interfaces:
CommandLine
,VcfAnnotator
public class VcfAnnotatorChain extends java.lang.Object implements VcfAnnotator
Maintains a list of VcfAnnotators and applies them one by one in the specified order
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Constructor Summary
Constructors Constructor Description VcfAnnotatorChain()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(VcfAnnotator vcfAnnotator)
Add a new annotatorboolean
addHeaders(VcfFileIterator vcfFile)
Add annotation headers to VCF fileboolean
annotate(VcfEntry vcfEntry)
Annotate a VCF file entryboolean
annotateFinish(VcfFileIterator vcf)
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.java.lang.String[]
getArgs()
void
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run the commandvoid
setConfig(Config config)
Set configurationvoid
setDebug(boolean debug)
Set debug modevoid
setVerbose(boolean verbose)
Set verbose modevoid
usage(java.lang.String message)
Show 'usage' message and exit with an error code '-1'
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Method Detail
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add
public void add(VcfAnnotator vcfAnnotator)
Add a new annotator
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addHeaders
public boolean addHeaders(VcfFileIterator vcfFile)
Description copied from interface:VcfAnnotator
Add annotation headers to VCF file- Specified by:
addHeaders
in interfaceVcfAnnotator
- Returns:
- true if OK, false on error
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annotate
public boolean annotate(VcfEntry vcfEntry)
Description copied from interface:VcfAnnotator
Annotate a VCF file entry- Specified by:
annotate
in interfaceVcfAnnotator
- Returns:
- true if the entry was annotated
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annotateFinish
public boolean annotateFinish(VcfFileIterator vcf)
Description copied from interface:VcfAnnotator
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).- Specified by:
annotateFinish
in interfaceVcfAnnotator
- Returns:
- true if OK, false on error
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annotateInit
public boolean annotateInit(VcfFileIterator vcfFile)
Description copied from interface:VcfAnnotator
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.- Specified by:
annotateInit
in interfaceVcfAnnotator
- Returns:
- true if OK, false on error
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getArgs
public java.lang.String[] getArgs()
- Specified by:
getArgs
in interfaceCommandLine
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parseArgs
public void parseArgs(java.lang.String[] args)
Description copied from interface:CommandLine
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
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run
public boolean run()
Description copied from interface:CommandLine
Run the command- Specified by:
run
in interfaceCommandLine
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setConfig
public void setConfig(Config config)
Description copied from interface:VcfAnnotator
Set configuration- Specified by:
setConfig
in interfaceVcfAnnotator
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setDebug
public void setDebug(boolean debug)
Description copied from interface:VcfAnnotator
Set debug mode- Specified by:
setDebug
in interfaceVcfAnnotator
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setVerbose
public void setVerbose(boolean verbose)
Description copied from interface:VcfAnnotator
Set verbose mode- Specified by:
setVerbose
in interfaceVcfAnnotator
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usage
public void usage(java.lang.String message)
Description copied from interface:CommandLine
Show 'usage' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
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