Package picard.sam
Class CalculateReadGroupChecksum
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.CalculateReadGroupChecksum
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@DocumentedFeature public class CalculateReadGroupChecksum extends CommandLineProgram
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Field Summary
Fields Modifier and Type Field Description File
INPUT
File
OUTPUT
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Fields 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, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CalculateReadGroupChecksum()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected 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
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Method Detail
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getOutputFileName
public 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.
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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.
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