Modifier and Type | Field and Description |
---|---|
protected JannovarOptions |
JannovarCommand.options
Configuration to use for the command execution.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
JannovarOptions |
AnnotatePositionCommandLineParser.parse(String[] argv) |
protected JannovarOptions |
AnnotatePositionCommand.parseCommandLine(String[] argv) |
Modifier and Type | Method and Description |
---|---|
JannovarOptions |
AnnotateVCFCommandLineParser.parse(String[] argv) |
protected JannovarOptions |
AnnotateVCFCommand.parseCommandLine(String[] argv) |
Constructor and Description |
---|
AnnotatedJannovarWriter(ReferenceDictionary refDict,
com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap,
String vcfPath,
JannovarOptions options) |
AnnotatedVCFWriter(ReferenceDictionary refDict,
htsjdk.variant.vcf.VCFFileReader reader,
com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap,
String vcfPath,
JannovarOptions options,
com.google.common.collect.ImmutableList<String> args) |
Modifier and Type | Method and Description |
---|---|
JannovarOptions |
DatabaseListCommandLineParser.parse(String[] argv)
Parse the command line and
|
protected JannovarOptions |
DatabaseListCommand.parseCommandLine(String[] argv) |
Modifier and Type | Method and Description |
---|---|
JannovarOptions |
DownloadCommandLineParser.parse(String[] argv)
Parse the command line and
|
protected JannovarOptions |
DownloadCommand.parseCommandLine(String[] argv) |
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