Package org.snpsift.caseControl

Class SnpSiftCmdCaseControlSummary

java.lang.Object

org.snpsift.SnpSift

org.snpsift.caseControl.SnpSiftCmdCaseControlSummary

All Implemented Interfaces:

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

public class SnpSiftCmdCaseControlSummary
extends SnpSift

Summarize a VCF annotated file

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.Boolean[]	CaseControl
static org.snpeff.vcf.EffFormatVersion	formatVersion

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
SnpSiftCmdCaseControlSummary()
SnpSiftCmdCaseControlSummary(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run summary
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

formatVersion

public static org.snpeff.vcf.EffFormatVersion formatVersion

CaseControl

public static java.lang.Boolean[] CaseControl

Constructor Detail

SnpSiftCmdCaseControlSummary

public SnpSiftCmdCaseControlSummary()

SnpSiftCmdCaseControlSummary

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

Method Detail

parseArgs

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

Description copied from class: SnpSift

Parse command line arguments

Specified by:

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

Overrides:

parseArgs in class SnpSift

run

public boolean run()

Run summary

Specified by:

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

Overrides:

run in class SnpSift

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

Parameters:

msg -