@DocumentedFeature public class IntervalListToBed extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
File |
INPUT |
|
File |
OUTPUT |
|
int |
SCORE |
|
boolean |
SORT |
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 |
|---|---|
IntervalListToBed() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(shortName="I",
doc="Input IntervalList file.")
public File INPUT
@Argument(shortName="O",
doc="Output BED file.")
public File OUTPUT
@Argument(doc="The score, between 0-1000, to output for each interval in the BED file.") public int SCORE
@Argument(doc="If true, sort the interval list prior to outputting as BED file.") public boolean SORT
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram