Package org.snpsift
Class SnpSiftCmdFilterGt
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdFilterGt
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Generic SnpSift genotype filter
Removes genotypes matching the filter:
e.g. if the expression is "GQ invalid input: '<' 20", all genotypes
with quality lower than 20 will be replaced
by './.' (missing)
- 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
Modifier and TypeMethodDescriptionvoid
Read a file as a string setList
<org.snpeff.vcf.VcfEntry> Filter a fileprotected List
<org.snpeff.vcf.VcfHeaderEntry> headers()
Headers to addvoid
init()
Initialize default valuesvoid
Parse command line optionsparseExpression
(String expression) Parse expressionboolean
run()
List
<org.snpeff.vcf.VcfEntry> run
(boolean createList) Run filtervoid
Usage messageMethods inherited from class org.snpsift.SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, isOpt, loadConfig, main, openVcfInputFile, processVcfHeader, setCommand, setCommand, setConfig, setConfigFile, setDbFileName, setDebug, setQuiet, setSaveOutput, setShowVcfHeader, setShowVersion, setSuppressOutput, setVcfHeaderAddProgramVersion, setVerbose, showCmd, showVersion, unSanitize, usageGenericAndDb
-
Constructor Details
-
SnpSiftCmdFilterGt
public SnpSiftCmdFilterGt() -
SnpSiftCmdFilterGt
-
-
Method Details
-
addSet
Read a file as a string set -
filter
Filter a file -
headers
Description copied from class:SnpSift
Headers to add -
init
public void init()Initialize default values -
parseArgs
Parse command line options -
parseExpression
Parse expression- Throws:
Exception
-
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
-