Package org.snpsift
Class SnpSiftCmdSort
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdSort
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Sort VCF file/s by chromosome invalid input: '&' position
- Author:
- pablocingolani
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Field Summary
FieldsFields 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
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 Details
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SHOW
public static final int SHOW- See Also:
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SHOW_LINES
public static final int SHOW_LINES- See Also:
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Constructor Details
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SnpSiftCmdSort
public SnpSiftCmdSort() -
SnpSiftCmdSort
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Method Details
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loadVcfFiles
public void loadVcfFiles()Load VCF files -
parseArgs
Parse command line arguments -
run
public boolean run()Run -
run
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usage
Show usage message
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