public class LiftOverIntervalList extends CommandLineProgram
Modifier and Type | Field | Description |
---|---|---|
File |
CHAIN |
|
File |
INPUT |
|
double |
MIN_LIFTOVER_PCT |
|
File |
OUTPUT |
|
File |
SEQUENCE_DICTIONARY |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor | Description |
---|---|
LiftOverIntervalList() |
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="Sequence dictionary to write into the output interval list.", shortName="SD") public File SEQUENCE_DICTIONARY
public static void main(String[] argv)
protected int doWork()
doWork
in class CommandLineProgram