@DocumentedFeature public class ConvertSequencingArtifactToOxoG extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
File |
INPUT_BASE |
|
File |
OUTPUT_BASE |
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 |
|---|---|
ConvertSequencingArtifactToOxoG() |
| 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="Basename of the input artifact metrics file (output by CollectSequencingArtifactMetrics)")
public File INPUT_BASE
@Argument(shortName="O",
doc="Basename for output OxoG metrics. Defaults to same basename as input metrics",
optional=true)
public File OUTPUT_BASE
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram