public class RenameSampleInVcf extends CommandLineProgram
Modifier and Type | Field and Description |
---|---|
java.io.File |
INPUT |
java.lang.String |
NEW_SAMPLE_NAME |
java.lang.String |
OLD_SAMPLE_NAME |
java.io.File |
OUTPUT |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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RenameSampleInVcf() |
Modifier and Type | Method and Description |
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protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(java.lang.String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="Existing name of sample in VCF; if provided, asserts that that is the name of the extant sample name", optional=true) public java.lang.String OLD_SAMPLE_NAME
public static void main(java.lang.String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram