Package org.snpsift
Class SnpSiftCmdFilterChrPos
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdFilterChrPos
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Filter using CHROM:POS only
- Author:
- pablocingolani
-
Field Summary
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 -
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
-
Constructor Details
-
SnpSiftCmdFilterChrPos
public SnpSiftCmdFilterChrPos() -
SnpSiftCmdFilterChrPos
-
-
Method Details
-
filter
protected boolean filter(org.snpeff.vcf.VcfEntry vcfEntry) Filter this line?- Returns:
- true if the filter is satisfied, false otherwise
-
parseArgs
Parse command line options -
run
public boolean run() -
run
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.
-
usage
Usage message
-