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
public class SnpSiftCmdSplit extends SnpSift
Split a large VCF file by chromosome or bby number of lines- Author:
- pablocingolani
-
-
Field Summary
Fields Modifier and Type Field Description static java.lang.String[]
exts
static int
SHOW
static int
SHOW_LINES
-
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
-
-
Constructor Summary
Constructors Constructor Description SnpSiftCmdSplit()
SnpSiftCmdSplit(java.lang.String[] args)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.ArrayList<java.lang.String>
getFileNames()
Names of files created when splittingjava.lang.String
join(boolean createString)
Join filesvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Runvoid
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
-
-
-
-
Field Detail
-
SHOW
public static final int SHOW
- See Also:
- Constant Field Values
-
SHOW_LINES
public static final int SHOW_LINES
- See Also:
- Constant Field Values
-
exts
public static java.lang.String[] exts
-
-
Method Detail
-
getFileNames
public java.util.ArrayList<java.lang.String> getFileNames()
Names of files created when splitting- Returns:
-
join
public java.lang.String join(boolean createString)
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
public void parseArgs(java.lang.String[] args)
Parse command line arguments
-
run
public boolean run()
Run
-
-