picard.sam

Class SortSam

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.SortSam

public class SortSam
extends CommandLineProgram

Author:

alecw@broadinstitute.org

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
java.io.File	OUTPUT
htsjdk.samtools.SAMFileHeader.SortOrder	SORT_ORDER

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
SortSam()

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="The BAM or SAM file to sort.",
        shortName="I")
public java.io.File INPUT

OUTPUT

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

SORT_ORDER

@Option(shortName="SO",
        doc="Sort order of output file")
public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER

Constructor Detail

SortSam

public SortSam()

Method Detail

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.