Package org.snpsift
Class SnpSiftCmdFilter
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdFilter
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- 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
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
VCF_INFO_FILTER_DELETED
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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
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Constructor Summary
Constructors Constructor Description SnpSiftCmdFilter()
SnpSiftCmdFilter(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addSet(java.lang.String fileName)
Read a file as a string setboolean
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 fileprotected java.util.List<org.snpeff.vcf.VcfHeaderEntry>
headers()
Headers to addvoid
init()
Initialize default valuesvoid
parseArgs(java.lang.String[] args)
Parse command line optionsExpression
parseExpression(java.lang.String expression)
Parse expressionboolean
run()
java.util.List<org.snpeff.vcf.VcfEntry>
run(boolean createList)
Run filtervoid
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
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Field Detail
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VCF_INFO_FILTER_DELETED
public static final java.lang.String VCF_INFO_FILTER_DELETED
- See Also:
- Constant Field Values
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Method Detail
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addSet
public void addSet(java.lang.String fileName)
Read a file as a string set
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)
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annotateInit
public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
- Specified by:
annotateInit
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
annotateInit
in classSnpSift
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filter
public java.util.List<org.snpeff.vcf.VcfEntry> filter(java.lang.String fileName, java.lang.String expression, boolean createList)
Filter a file
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headers
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
Description copied from class:SnpSift
Headers to add
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line options
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parseExpression
public Expression parseExpression(java.lang.String expression) throws java.lang.Exception
Parse expression- Throws:
java.lang.Exception
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run
public boolean run()
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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.
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setAddFilterField
public void setAddFilterField(java.lang.String addFilterField)
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setExceptionIfNotFound
public void setExceptionIfNotFound(boolean exceptionIfNotFound)
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setExpression
public void setExpression(java.lang.String expression)
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setFilterId
public void setFilterId(java.lang.String filterId)
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setFormatVersion
public void setFormatVersion(org.snpeff.vcf.EffFormatVersion formatVersion)
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setInverse
public void setInverse(boolean inverse)
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setRmFilterField
public void setRmFilterField(java.lang.String rmFilterField)
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setSets
public void setSets(java.util.ArrayList<java.util.HashSet<java.lang.String>> sets)
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setUsePassField
public void setUsePassField(boolean usePassField)
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