@DocumentedFeature public class NormalizeFasta extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
File |
INPUT |
|
int |
LINE_LENGTH |
|
File |
OUTPUT |
|
boolean |
TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE |
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 |
|---|---|
NormalizeFasta() |
| 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 FASTA file to normalize.")
public File INPUT
@Argument(shortName="O",
doc="The output FASTA file to write.")
public File OUTPUT
@Argument(doc="The line length to be used for the output FASTA file.") public int LINE_LENGTH
@Argument(doc="Truncate sequence names at first whitespace.") public boolean TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE
public static void main(String[] args)
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram