picard.sam

Class SetNmAndUqTags

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.SetNmAndUqTags

public class SetNmAndUqTags
extends CommandLineProgram

Author:

Yossi Farjoun

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
boolean	IS_BISULFITE_SEQUENCE
java.io.File	OUTPUT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
SetNmAndUqTags()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] argv)

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Option(doc="The BAM or SAM file to fix.",
        shortName="I")
public java.io.File INPUT

OUTPUT

@Option(doc="The fixed BAM or SAM output file. ",
        shortName="O")
public java.io.File OUTPUT

IS_BISULFITE_SEQUENCE

@Option(doc="Whether the file contains bisulfite sequence (used when calculating the NM tag).")
public boolean IS_BISULFITE_SEQUENCE

Constructor Detail

SetNmAndUqTags

public SetNmAndUqTags()

Method Detail

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

main

public static void main(java.lang.String[] argv)

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.