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
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
FieldsModifier and TypeFieldDescriptionprotected org.snpeff.vcf.VcfEntry
static final String
static final String
static final String
static final String
static final int
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 -
Method Summary
Modifier and TypeMethodDescriptionorg.snpeff.stats.CountByType
org.snpeff.collections.AutoHashMap
<String, org.snpeff.stats.CountByType> int
void
init()
Initialize default valuesvoid
Parse command line argumentsboolean
run()
void
setWriteBySampleFile
(boolean writeBySampleFile) void
setWriteSummaryFile
(boolean writeSummaryFile) void
Show usage messageMethods 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 Details
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MISSING_GENOTYPE
- See Also:
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MISSING_ENTRY
- See Also:
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SEP
- See Also:
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SEP_GT
- See Also:
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SHOW_EVERY
public static final int SHOW_EVERY- See Also:
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latestVcfEntry
protected org.snpeff.vcf.VcfEntry latestVcfEntry
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Constructor Details
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SnpSiftCmdConcordance
public SnpSiftCmdConcordance() -
SnpSiftCmdConcordance
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Method Details
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getConcordance
public org.snpeff.stats.CountByType getConcordance() -
getConcordanceBySample
public org.snpeff.collections.AutoHashMap<String,org.snpeff.stats.CountByType> getConcordanceBySample() -
getCountEntries
public int getCountEntries() -
init
public void init()Description copied from class:SnpSift
Initialize default values -
parseArgs
Parse command line arguments -
run
public boolean run() -
setWriteBySampleFile
public void setWriteBySampleFile(boolean writeBySampleFile) -
setWriteSummaryFile
public void setWriteSummaryFile(boolean writeSummaryFile) -
usage
Show usage message
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