@DocumentedFeature public class SplitVcfs extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
File |
INDEL_OUTPUT |
|
File |
INPUT |
|
File |
SEQUENCE_DICTIONARY |
|
File |
SNP_OUTPUT |
|
Boolean |
STRICT |
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 |
|---|---|
SplitVcfs() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] argv) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(shortName="I",
doc="The VCF or BCF input file")
public File INPUT
@Argument(doc="The VCF or BCF file to which SNP records should be written. The file format is determined by file extension.") public File SNP_OUTPUT
@Argument(doc="The VCF or BCF file to which indel records should be written. The file format is determined by file extension.") public File INDEL_OUTPUT
@Argument(shortName="D",
doc="The index sequence dictionary to use instead of the sequence dictionaries in the input files",
optional=true)
public File SEQUENCE_DICTIONARY
@Argument(doc="If true an exception will be thrown if an event type other than SNP or indel is encountered") public Boolean STRICT
public static void main(String[] argv)
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram