Package org.snpsift
Class SnpSiftCmdSplit
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdSplit
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Split a large VCF file by chromosome or bby number of lines
- Author:
- pablocingolani
-
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
-
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
-
Field Details
-
SHOW
public static final int SHOW- See Also:
-
SHOW_LINES
public static final int SHOW_LINES- See Also:
-
exts
-
-
Constructor Details
-
SnpSiftCmdSplit
public SnpSiftCmdSplit() -
SnpSiftCmdSplit
-
-
Method Details
-
getFileNames
Names of files created when splitting- Returns:
-
join
Join files- Parameters:
createString
- : Create a string used for test cases)- Returns:
- A string with the resulting file if createString is true. An empty string otherwise.
-
parseArgs
Parse command line arguments -
run
public boolean run()Run -
usage
Show usage message
-