Package org.snpsift
Class SnpSiftCmdFilterChrPos
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdFilterChrPos
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdFilterChrPos extends SnpSift
Filter using CHROM:POS only- Author:
- pablocingolani
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Field Summary
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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 SnpSiftCmdFilterChrPos()
SnpSiftCmdFilterChrPos(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
filter(org.snpeff.vcf.VcfEntry vcfEntry)
Filter this line?void
parseArgs(java.lang.String[] args)
Parse command line optionsboolean
run()
java.util.List<org.snpeff.vcf.VcfEntry>
run(boolean createList)
Run filtervoid
usage(java.lang.String msg)
Usage message-
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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Method Detail
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filter
protected boolean filter(org.snpeff.vcf.VcfEntry vcfEntry)
Filter this line?- Returns:
- true if the filter is satisfied, false otherwise
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line options
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run
public boolean run()
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run
public java.util.List<org.snpeff.vcf.VcfEntry> run(boolean createList)
Run filter- Parameters:
createList
- : If true, create a list with the results. If false, show results on STDOUT- Returns:
- If 'createList' is true, return a list containing all vcfEntries that passed the filter. Otherwise return null.
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