picard.sam

Class ReplaceSamHeader

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.ReplaceSamHeader

public class ReplaceSamHeader
extends CommandLineProgram

Author:

alecw@broadinstitute.org

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	HEADER
java.io.File	INPUT
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
ReplaceSamHeader()

Method Summary

Modifier and Type	Method and Description
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

customCommandLineValidation, 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="SAM file from which SAMRecords will be read.",
        shortName="I")
public java.io.File INPUT

HEADER

@Option(doc="SAM file from which SAMFileHeader will be read.")
public java.io.File HEADER

OUTPUT

@Option(doc="SAMFileHeader from HEADER file will be written to this file, followed by SAMRecords from INPUT file",
        shortName="O")
public java.io.File OUTPUT

Constructor Detail

ReplaceSamHeader

public ReplaceSamHeader()

Method Detail

main

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

doWork

protected int doWork()

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.