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, TMP_DIR, 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, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(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
@Option(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
@Option(shortName="D", doc="The index sequence dictionary to use instead of the sequence dictionaries in the input files", optional=true) public File SEQUENCE_DICTIONARY
public static void main(String[] argv)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram