picard.vcf

Class SortVcf

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.SortVcf

public class SortVcf
extends CommandLineProgram

Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate. Can accept an external dictionary. If no external dictionary is supplied, multiple inputs' headers must have the same sequence dictionaries

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.io.File>	INPUT
java.io.File	OUTPUT
java.io.File	SEQUENCE_DICTIONARY

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
SortVcf()

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[] args)

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(shortName="I",
        doc="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)")
public java.util.List<java.io.File> INPUT

OUTPUT

@Option(shortName="O",
        doc="Output VCF to be written.")
public java.io.File OUTPUT

SEQUENCE_DICTIONARY

@Option(shortName="SD",
        optional=true)
public java.io.File SEQUENCE_DICTIONARY

Constructor Detail

SortVcf

public SortVcf()

Method Detail

main

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

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.