Package org.snpsift
Class SnpSiftCmdRemoveReferenceGenotypes
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
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- 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
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Field Summary
Fields Modifier and Type Field Description static int
SHOW_EVERY
static int
SHOW_EVERY_NL
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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 SnpSiftCmdRemoveReferenceGenotypes()
SnpSiftCmdRemoveReferenceGenotypes(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Analyze the filevoid
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
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Field Detail
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SHOW_EVERY
public static final int SHOW_EVERY
- See Also:
- Constant Field Values
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SHOW_EVERY_NL
public static final int SHOW_EVERY_NL
- See Also:
- Constant Field Values
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Method Detail
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parseArgs
public void parseArgs(java.lang.String[] args)
Description copied from class:SnpSift
Parse command line arguments
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run
public boolean run()
Analyze the file
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