Package org.snpsift
Class SnpSiftCmdSort
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdSort
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdSort extends SnpSift
Sort VCF file/s by chromosome & position- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static int
SHOW
static int
SHOW_LINES
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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 SnpSiftCmdSort()
SnpSiftCmdSort(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
loadVcfFiles()
Load VCF filesvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Runjava.util.List<org.snpeff.vcf.VcfEntry>
run(boolean createList)
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, 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
public static final int SHOW
- See Also:
- Constant Field Values
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SHOW_LINES
public static final int SHOW_LINES
- See Also:
- Constant Field Values
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