Package org.snpsift

Class SnpSiftCmdConcordance

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdConcordance

All Implemented Interfaces:

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

public class SnpSiftCmdConcordance
extends SnpSift

Calculate genotyping concordance between two VCF files. Typical usage: Calculate concordance between sequencing experiment and genotypting experiment.

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
protected org.snpeff.vcf.VcfEntry	latestVcfEntry
static java.lang.String	MISSING_ENTRY
static java.lang.String	MISSING_GENOTYPE
static java.lang.String	SEP
static java.lang.String	SEP_GT
static int	SHOW_EVERY

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

Method Summary

Modifier and Type	Method	Description
org.snpeff.stats.CountByType	getConcordance()
org.snpeff.collections.AutoHashMap<java.lang.String,org.snpeff.stats.CountByType>	getConcordanceBySample()
int	getCountEntries()
void	init()	Initialize default values
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()
void	setWriteBySampleFile(boolean writeBySampleFile)
void	setWriteSummaryFile(boolean writeSummaryFile)
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, 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

MISSING_GENOTYPE

public static final java.lang.String MISSING_GENOTYPE

See Also:

Constant Field Values

MISSING_ENTRY

public static final java.lang.String MISSING_ENTRY

See Also:

Constant Field Values

SEP

public static final java.lang.String SEP

See Also:

Constant Field Values

SEP_GT

public static final java.lang.String SEP_GT

See Also:

Constant Field Values

SHOW_EVERY

public static final int SHOW_EVERY

See Also:

Constant Field Values

latestVcfEntry

protected org.snpeff.vcf.VcfEntry latestVcfEntry

Constructor Detail

SnpSiftCmdConcordance

public SnpSiftCmdConcordance()

SnpSiftCmdConcordance

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

Method Detail

getConcordance

public org.snpeff.stats.CountByType getConcordance()

getConcordanceBySample

public org.snpeff.collections.AutoHashMap<java.lang.String,org.snpeff.stats.CountByType> getConcordanceBySample()

getCountEntries

public int getCountEntries()

init

public void init()

Description copied from class: SnpSift

Initialize default values

Overrides:

init in class SnpSift

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()

Specified by:

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

Overrides:

run in class SnpSift

setWriteBySampleFile

public void setWriteBySampleFile(boolean writeBySampleFile)

setWriteSummaryFile

public void setWriteSummaryFile(boolean writeSummaryFile)

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