@DocumentedFeature public class ReplaceSamHeader extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
File |
HEADER |
|
File |
INPUT |
|
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 |
|---|---|
ReplaceSamHeader() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] argv) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(doc="SAM file from which SAMRecords will be read.",
shortName="I")
public File INPUT
@Argument(doc="SAM file from which SAMFileHeader will be read.") public File HEADER
@Argument(doc="SAMFileHeader from HEADER file will be written to this file, followed by SAMRecords from INPUT file",
shortName="O")
public File OUTPUT
public static void main(String[] argv)
protected int doWork()
doWork in class CommandLineProgram