Package picard.sam.markduplicates

Class CheckDuplicateMarking

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.markduplicates.CheckDuplicateMarking

@DocumentedFeature(enable=false)
public class CheckDuplicateMarking
extends CommandLineProgram

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	CheckDuplicateMarking.Mode

Field Summary

Fields

Modifier and Type	Field	Description
File	INPUT
CheckDuplicateMarking.Mode	MODE
File	OUTPUT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, 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

Constructor	Description
CheckDuplicateMarking()

Method Summary

Modifier and Type	Method	Description
protected int	doWork()	Do the work after command line has been parsed.

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

Methods inherited from class java.lang.Object

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

Field Details

INPUT

@Argument(doc="Input BAM or SAM file to check.",
          shortName="I")
public File INPUT

OUTPUT

@Argument(doc="Output file into which bad querynames will be placed (if not null).",
          shortName="O",
          optional=true)
public File OUTPUT

MODE

@Argument(doc="Which reads of the same name should be checked to have same duplicate marking.")
public CheckDuplicateMarking.Mode MODE

Constructor Details

CheckDuplicateMarking

public CheckDuplicateMarking()

Method Details

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 class CommandLineProgram

Returns:

program exit status.