@DocumentedFeature public class UpdateVcfSequenceDictionary extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
File |
INPUT |
|
File |
OUTPUT |
|
File |
SEQUENCE_DICTIONARY |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY| Constructor | Description |
|---|---|
UpdateVcfSequenceDictionary() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(shortName="I",
doc="Input VCF")
public File INPUT
@Argument(shortName="O",
doc="Output VCF to be written.")
public File OUTPUT
@Argument(shortName="SD",
doc="A Sequence Dictionary (can be read from one of the following file types (SAM, BAM, VCF, BCF, Interval List, Fasta, or Dict)")
public File SEQUENCE_DICTIONARY
public static void main(String[] args)
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram