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

public class SnpSiftCmdFilterGt
extends SnpSift

Generic SnpSift genotype filter Removes genotypes matching the filter: e.g. if the expression is "GQ < 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

Constructor	Description
SnpSiftCmdFilterGt()
SnpSiftCmdFilterGt(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
void	addSet(java.lang.String fileName)	Read a file as a string set
java.util.List<org.snpeff.vcf.VcfEntry>	filter(java.lang.String fileName, java.lang.String expression, boolean createList)	Filter a file
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>	headers()	Headers to add
void	init()	Initialize default values
void	parseArgs(java.lang.String[] args)	Parse command line options
Expression	parseExpression(java.lang.String expression)	Parse expression
boolean	run()
java.util.List<org.snpeff.vcf.VcfEntry>	run(boolean createList)	Run filter
void	usage(java.lang.String msg)	Usage message

Methods 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SnpSiftCmdFilterGt

public SnpSiftCmdFilterGt()

SnpSiftCmdFilterGt

public SnpSiftCmdFilterGt(java.lang.String[] args)

Method Detail

addSet

public void addSet(java.lang.String fileName)

Read a file as a string set

filter

public java.util.List<org.snpeff.vcf.VcfEntry> filter(java.lang.String fileName,
                                                      java.lang.String expression,
                                                      boolean createList)

Filter a file

headers

protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()

Description copied from class: SnpSift

Headers to add

Overrides:

headers in class SnpSift

init

public void init()

Initialize default values

Overrides:

init in class SnpSift

parseArgs

public void parseArgs(java.lang.String[] args)

Parse command line options

Specified by:

parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

parseArgs in class SnpSift

parseExpression

public Expression parseExpression(java.lang.String expression)
                           throws java.lang.Exception

Parse expression

Throws:

java.lang.Exception

run

public boolean run()

Specified by:

run in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

run in class SnpSift

run

public java.util.List<org.snpeff.vcf.VcfEntry> run(boolean createList)

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

public void usage(java.lang.String msg)

Usage message

Specified by:

usage in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

usage in class SnpSift