public class VcfFormatConverter extends CommandLineProgram
Modifier and Type | Field and Description |
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File |
INPUT |
static Log |
LOG |
File |
OUTPUT |
Boolean |
REQUIRE_INDEX |
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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VcfFormatConverter() |
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(String[] argv) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
public static final Log LOG
@Option(doc="The BCF or VCF input file. The file format is determined by file extension.", shortName="I") public File INPUT
@Option(doc="The BCF or VCF output file. The file format is determined by file extension.", shortName="O") public File OUTPUT
public static void main(String[] argv)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram