Modifier and Type | Method and Description |
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protected void |
JannovarAnnotationCommand.deserializeTranscriptDefinitionFile()
Deserialize the transcript definition file, as configured in
JannovarCommand.options . |
abstract JannovarOptions |
JannovarAnnotationCommandLineParser.parse(String[] argv)
Parse command line arguments and return
JannovarOptions . |
protected abstract JannovarOptions |
JannovarCommand.parseCommandLine(String[] argv)
Function for parsing the command line.
|
protected void |
JannovarAnnotationCommandLineParser.printHelpIfOptionIsSet(org.apache.commons.cli.CommandLine cmd) |
Constructor and Description |
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JannovarAnnotationCommand(String[] argv) |
JannovarCommand(String[] argv)
Initialize the JannovarCommand.
|
Modifier and Type | Method and Description |
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JannovarOptions |
AnnotatePositionCommandLineParser.parse(String[] argv) |
protected JannovarOptions |
AnnotatePositionCommand.parseCommandLine(String[] argv) |
Constructor and Description |
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AnnotatePositionCommand(String[] argv) |
Modifier and Type | Method and Description |
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JannovarOptions |
AnnotateVCFCommandLineParser.parse(String[] argv) |
protected JannovarOptions |
AnnotateVCFCommand.parseCommandLine(String[] argv) |
Constructor and Description |
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AnnotateVCFCommand(String[] argv) |
Modifier and Type | Method and Description |
---|---|
JannovarOptions |
DatabaseListCommandLineParser.parse(String[] argv)
Parse the command line and
|
protected JannovarOptions |
DatabaseListCommand.parseCommandLine(String[] argv) |
Constructor and Description |
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DatabaseListCommand(String[] argv) |
Modifier and Type | Method and Description |
---|---|
JannovarOptions |
DownloadCommandLineParser.parse(String[] argv)
Parse the command line and
|
protected JannovarOptions |
DownloadCommand.parseCommandLine(String[] argv) |
Constructor and Description |
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DownloadCommand(String[] argv) |
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