Package org.snpsift

Class SnpSiftCmdFilter

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdFilter

All Implemented Interfaces:

org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdFilter
extends SnpSift

Generic SnpSift filter Filter out data based on VCF attributes: - Chromosome, Position, etc. - Intersecting intervals (BED file) - Quality, Coverage, etc. - Any INFO field - Parse expression - Int, double fields: FiledZZ == N, FiledZZ < X, FiledZZ > X, FiledZZ <= X, FiledZZ >= X - String: FiledZZ eq "someString", FiledZZ =~ "some*regex$" - Samples informations - s50 (SNPs that appear in 50% of samples or more) - Singletons - Doubletons - Tripletons - negate all previous expressions - pValue (Fisher exact test) - Database information - Known (e.g. in dbSnp) - Novel (e.g. NOT in dbSnp)

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	VCF_INFO_FILTER_DELETED

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
SnpSiftCmdFilter()
SnpSiftCmdFilter(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
void	addSet(java.lang.String fileName)	Read a file as a string set
boolean	annotate(org.snpeff.vcf.VcfEntry vcfEntry)
boolean	annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
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	setAddFilterField(java.lang.String addFilterField)
void	setExceptionIfNotFound(boolean exceptionIfNotFound)
void	setExpression(java.lang.String expression)
void	setFilterId(java.lang.String filterId)
void	setFormatVersion(org.snpeff.vcf.EffFormatVersion formatVersion)
void	setInverse(boolean inverse)
void	setRmFilterField(java.lang.String rmFilterField)
void	setSets(java.util.ArrayList<java.util.HashSet<java.lang.String>> sets)
void	setUsePassField(boolean usePassField)
void	usage(java.lang.String msg)	Usage message

Methods inherited from class org.snpsift.SnpSift

addHeaders, annotateFinish, 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

Field Detail

VCF_INFO_FILTER_DELETED

public static final java.lang.String VCF_INFO_FILTER_DELETED

See Also:

Constant Field Values

Constructor Detail

SnpSiftCmdFilter

public SnpSiftCmdFilter()

SnpSiftCmdFilter

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

Method Detail

addSet

public void addSet(java.lang.String fileName)

Read a file as a string set

annotate

public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)

Specified by:

annotate in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotate in class SnpSift

annotateInit

public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)

Specified by:

annotateInit in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotateInit in class SnpSift

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.

setAddFilterField

public void setAddFilterField(java.lang.String addFilterField)

setExceptionIfNotFound

public void setExceptionIfNotFound(boolean exceptionIfNotFound)

setExpression

public void setExpression(java.lang.String expression)

setFilterId

public void setFilterId(java.lang.String filterId)

setFormatVersion

public void setFormatVersion(org.snpeff.vcf.EffFormatVersion formatVersion)

setInverse

public void setInverse(boolean inverse)

setRmFilterField

public void setRmFilterField(java.lang.String rmFilterField)

setSets

public void setSets(java.util.ArrayList<java.util.HashSet<java.lang.String>> sets)

setUsePassField

public void setUsePassField(boolean usePassField)

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