Package org.snpsift

Class SnpSiftCmdRemoveReferenceGenotypes

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdRemoveReferenceGenotypes

All Implemented Interfaces:

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

public class SnpSiftCmdRemoveReferenceGenotypes
extends SnpSift

Removes reference genotypes. I.e. replaces the genotype string by the MISSING string ('.') if the genotype is just homozygous reference (e.g. '0/0')

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
static int	SHOW_EVERY
static int	SHOW_EVERY_NL

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

Method Summary

Modifier and Type	Method	Description
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Analyze the file
void	usage(java.lang.String errMsg)	Show usage and exit

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_EVERY

public static final int SHOW_EVERY

See Also:

Constant Field Values

SHOW_EVERY_NL

public static final int SHOW_EVERY_NL

See Also:

Constant Field Values

Constructor Detail

SnpSiftCmdRemoveReferenceGenotypes

public SnpSiftCmdRemoveReferenceGenotypes()

SnpSiftCmdRemoveReferenceGenotypes

public SnpSiftCmdRemoveReferenceGenotypes(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()

Analyze the file

Specified by:

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

Overrides:

run in class SnpSift

usage

public void usage(java.lang.String errMsg)

Show usage and exit

Specified by:

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

Overrides:

usage in class SnpSift