Package picard.sam
Class CalculateReadGroupChecksum
java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.CalculateReadGroupChecksum
-
Field Summary
FieldsFields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.static String
getOutputFileName
(File inputFile) Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
Field Details
-
INPUT
-
OUTPUT
@Argument(shortName="O", doc="The file to which the hash code should be written.", optional=true) public File OUTPUT
-
-
Constructor Details
-
CalculateReadGroupChecksum
public CalculateReadGroupChecksum()
-
-
Method Details
-
getOutputFileName
Creates a file name (not including the path) for an RG MD5 file based on the name of the input file. -
doWork
protected int doWork()Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
-