Package org.snpeff.snpEffect
Interface VcfAnnotator
-
- All Superinterfaces:
CommandLine
- All Known Implementing Classes:
SnpEffCmdEff
,VcfAnnotatorChain
public interface VcfAnnotator extends CommandLine
Annotate a VCF file: E.g. add information to INFO column
-
-
Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description boolean
addHeaders(VcfFileIterator vcfFile)
Add annotation headers to VCF fileboolean
annotate(VcfEntry vcfEntry)
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
setConfig(Config config)
Set configurationvoid
setDebug(boolean debug)
Set debug modevoid
setVerbose(boolean verbose)
Set verbose mode-
Methods inherited from interface org.snpeff.snpEffect.commandLine.CommandLine
getArgs, parseArgs, run, usage
-
-
-
-
Method Detail
-
addHeaders
boolean addHeaders(VcfFileIterator vcfFile)
Add annotation headers to VCF file- Returns:
- true if OK, false on error
-
annotate
boolean annotate(VcfEntry vcfEntry)
Annotate a VCF file entry- Returns:
- true if the entry was annotated
-
annotateFinish
boolean annotateFinish(VcfFileIterator vcfFile)
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
-
annotateInit
boolean annotateInit(VcfFileIterator vcfFile)
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
-
setConfig
void setConfig(Config config)
Set configuration
-
setDebug
void setDebug(boolean debug)
Set debug mode
-
setVerbose
void setVerbose(boolean verbose)
Set verbose mode
-
-