@DocumentedFeature public class BedToIntervalList extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
File |
INPUT |
|
File |
OUTPUT |
|
File |
SEQUENCE_DICTIONARY |
|
boolean |
SORT |
|
boolean |
UNIQUE |
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 |
|---|---|
BedToIntervalList() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(shortName="I",
doc="The input BED file")
public File INPUT
@Argument(shortName="SD",
doc="The sequence dictionary, or BAM/VCF/IntervalList from which a dictionary can be extracted.")
public File SEQUENCE_DICTIONARY
@Argument(shortName="O",
doc="The output Picard Interval List")
public File OUTPUT
@Argument(doc="If true, sort the output interval list before writing it.") public boolean SORT
@Argument(doc="If true, unique the output interval list by merging overlapping regions, before writing it (implies sort=true).") public boolean UNIQUE
public static void main(String[] args)
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram