public class AnnotateVCFCommand extends JannovarAnnotationCommand
chromosomeMap, refDict
args, options, verbosity
Constructor and Description |
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AnnotateVCFCommand(String[] argv) |
Modifier and Type | Method and Description |
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protected JannovarOptions |
parseCommandLine(String[] argv)
Function for parsing the command line.
|
void |
run()
This function inputs a VCF file, and prints the annotated version thereof to a file (name of the original file
with the suffix .de.charite.compbio.jannovar).
|
deserializeTranscriptDefinitionFile
public AnnotateVCFCommand(String[] argv) throws CommandLineParsingException, HelpRequestedException
public void run() throws JannovarException
run
in class JannovarCommand
JannovarException
- on problems with the annotationprotected JannovarOptions parseCommandLine(String[] argv) throws CommandLineParsingException, HelpRequestedException
JannovarCommand
parseCommandLine
in class JannovarCommand
argv
- command line to parse, as in the program's main functionJannovarOptions
with the programs' configurationCommandLineParsingException
- on problems with the command lineHelpRequestedException
- when the user requested the help pageCopyright © 2016. All rights reserved.