Package org.snpsift
Class SnpSiftCmdConcordance
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdConcordance
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- 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
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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
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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
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Constructor Summary
Constructors Constructor Description SnpSiftCmdConcordance()
SnpSiftCmdConcordance(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods 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 valuesvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
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
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Field Detail
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MISSING_GENOTYPE
public static final java.lang.String MISSING_GENOTYPE
- See Also:
- Constant Field Values
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MISSING_ENTRY
public static final java.lang.String MISSING_ENTRY
- See Also:
- Constant Field Values
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SEP
public static final java.lang.String SEP
- See Also:
- Constant Field Values
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SEP_GT
public static final java.lang.String SEP_GT
- See Also:
- Constant Field Values
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SHOW_EVERY
public static final int SHOW_EVERY
- See Also:
- Constant Field Values
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latestVcfEntry
protected org.snpeff.vcf.VcfEntry latestVcfEntry
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Method Detail
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getConcordance
public org.snpeff.stats.CountByType getConcordance()
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getConcordanceBySample
public org.snpeff.collections.AutoHashMap<java.lang.String,org.snpeff.stats.CountByType> getConcordanceBySample()
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getCountEntries
public int getCountEntries()
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init
public void init()
Description copied from class:SnpSift
Initialize default values
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments
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run
public boolean run()
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setWriteBySampleFile
public void setWriteBySampleFile(boolean writeBySampleFile)
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setWriteSummaryFile
public void setWriteSummaryFile(boolean writeSummaryFile)
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