Field Summary

• Fields inherited from class picard.cmdline.CommandLineProgram

  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

• Fields inherited from class picard.sam.SetNmMdAndUqTags

  INPUT, IS_BISULFITE_SEQUENCE, OUTPUT, SET_ONLY_UQ

Constructor Summary

Method Summary

• Methods inherited from class picard.cmdline.CommandLineProgram

  customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser

• Methods inherited from class java.lang.Object

  clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

• Methods inherited from class picard.sam.SetNmMdAndUqTags

  doWork, main, requiresReference