public class SplitSamByLibrary extends CommandLineProgram
Modifier and Type | Field and Description |
---|---|
File |
INPUT |
static int |
NO_LIBRARIES_SPECIFIED_IN_HEADER |
File |
OUTPUT |
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 |
---|
SplitSamByLibrary() |
Modifier and Type | Method and Description |
---|---|
protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="O", doc="The directory where the library SAM or BAM files should be written (defaults to the current directory). ", optional=true) public File OUTPUT
public static final int NO_LIBRARIES_SPECIFIED_IN_HEADER
public static void main(String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram