@DocumentedFeature public class ExtractSequences extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
File |
INTERVAL_LIST |
|
int |
LINE_LENGTH |
|
File |
OUTPUT |
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 |
|---|---|
ExtractSequences() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
|
protected boolean |
requiresReference() |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser@Argument(doc="Interval list describing intervals to be extracted from the reference sequence.") public File INTERVAL_LIST
@Argument(shortName="O",
doc="Output FASTA file.")
public File OUTPUT
@Argument(doc="Maximum line length for sequence data.") public int LINE_LENGTH
public static void main(String[] args)
protected boolean requiresReference()
requiresReference in class CommandLineProgramprotected int doWork()
CommandLineProgramdoWork in class CommandLineProgram