Package org.snpsift

Class SnpSiftCmdSort

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdSort

All Implemented Interfaces:

org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdSort
extends SnpSift

Sort VCF file/s by chromosome & position

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
static int	SHOW
static int	SHOW_LINES

Fields inherited from class org.snpsift.SnpSift

args, BUILD, command, config, configFile, dataDir, dbFileName, dbTabix, dbType, debug, download, EMPTY_ARGS, errCount, genomeVersion, help, log, needsConfig, needsDb, needsGenome, numWorkers, output, quiet, REVISION, saveOutput, shiftArgs, SHOW_EVERY_VCFLINES, showVcfHeader, showVersion, SOFTWARE_NAME, suppressOutput, vcfHeaderAddProgramVersion, vcfHeaderProcessed, vcfInputFile, verbose, VERSION, VERSION_MAJOR, VERSION_NO_NAME, VERSION_SHORT

Constructor Summary

Constructors

Constructor	Description
SnpSiftCmdSort()
SnpSiftCmdSort(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
void	loadVcfFiles()	Load VCF files
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run
java.util.List<org.snpeff.vcf.VcfEntry>	run(boolean createList)
void	usage(java.lang.String msg)	Show usage message

Methods inherited from class org.snpsift.SnpSift

addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, init, isOpt, loadConfig, main, openVcfInputFile, processVcfHeader, setCommand, setCommand, setConfig, setConfigFile, setDbFileName, setDebug, setQuiet, setSaveOutput, setShowVcfHeader, setShowVersion, setSuppressOutput, setVcfHeaderAddProgramVersion, setVerbose, showCmd, showVersion, unSanitize, usageGenericAndDb

Methods inherited from class java.lang.Object

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

Field Detail

SHOW

public static final int SHOW

See Also:

Constant Field Values

SHOW_LINES

public static final int SHOW_LINES

See Also:

Constant Field Values

Constructor Detail

SnpSiftCmdSort

public SnpSiftCmdSort()

SnpSiftCmdSort

public SnpSiftCmdSort(java.lang.String[] args)

Method Detail

loadVcfFiles

public void loadVcfFiles()

Load VCF files

parseArgs

public void parseArgs(java.lang.String[] args)

Parse command line arguments

Specified by:

parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

parseArgs in class SnpSift

run

public boolean run()

Run

Specified by:

run in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

run in class SnpSift

run

public java.util.List<org.snpeff.vcf.VcfEntry> run(boolean createList)

usage

public void usage(java.lang.String msg)

Show usage message

Specified by:

usage in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

usage in class SnpSift