public class SplitVcfs extends CommandLineProgram
Modifier and Type | Field and Description |
---|---|
java.io.File |
INDEL_OUTPUT |
java.io.File |
INPUT |
java.io.File |
SEQUENCE_DICTIONARY |
java.io.File |
SNP_OUTPUT |
java.lang.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 and Description |
---|
SplitVcfs() |
Modifier and Type | Method and Description |
---|---|
protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(java.lang.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 java.io.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 java.io.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 java.io.File SEQUENCE_DICTIONARY
public static void main(java.lang.String[] argv)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram