Package org.snpsift

Class SnpSiftCmdVcfOperator

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdVcfOperator

All Implemented Interfaces:

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

public class SnpSiftCmdVcfOperator
extends SnpSift

Annotate a field based on an operation (max, min, etc.) of other VCF fields

Author:

pcingola

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SnpSiftCmdVcfOperator.Operator

Field Summary

Fields

Modifier and Type	Field	Description
protected java.lang.String	fields
protected java.lang.String[]	infoFields
protected SnpSiftCmdVcfOperator.Operator	operator
protected java.lang.String	outField

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

Method Summary

Modifier and Type	Method	Description
boolean	annotate(org.snpeff.vcf.VcfEntry vcfEntry)
java.lang.Double	applyOp(java.util.List<java.lang.Double> vals)
java.lang.String[]	getArgs()
java.util.List<java.lang.Double>	getValues(org.snpeff.vcf.VcfEntry vcfEntry)
java.util.List<java.lang.Double>	getValues(org.snpeff.vcf.VcfEntry vcfEntry, java.lang.String field)	Parse an INFO field (can be multiple valued) and return a list of Double
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>	headers()	Headers to add
protected double	initialValue()
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Annotate
java.util.List<org.snpeff.vcf.VcfEntry>	run(boolean createList)	Run filter
void	usage(java.lang.String msg)	Show usage message

Methods inherited from class org.snpsift.SnpSift

addHeaders, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getConfig, getConfigFile, getOutput, init, 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

fields

protected java.lang.String fields

outField

protected java.lang.String outField

operator

protected SnpSiftCmdVcfOperator.Operator operator

infoFields

protected java.lang.String[] infoFields

Constructor Detail

SnpSiftCmdVcfOperator

public SnpSiftCmdVcfOperator()

SnpSiftCmdVcfOperator

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

Method Detail

annotate

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

Specified by:

annotate in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotate in class SnpSift

applyOp

public java.lang.Double applyOp(java.util.List<java.lang.Double> vals)

getArgs

public java.lang.String[] getArgs()

Specified by:

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

Overrides:

getArgs in class SnpSift

getValues

public java.util.List<java.lang.Double> getValues(org.snpeff.vcf.VcfEntry vcfEntry)

getValues

public java.util.List<java.lang.Double> getValues(org.snpeff.vcf.VcfEntry vcfEntry,
                                                  java.lang.String field)

Parse an INFO field (can be multiple valued) and return a list of Double

headers

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

Description copied from class: SnpSift

Headers to add

Overrides:

headers in class SnpSift

initialValue

protected double initialValue()

parseArgs

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

Description copied from class: SnpSift

Parse command line arguments

Specified by:

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

Overrides:

parseArgs in class SnpSift

run

public boolean run()

Annotate

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)

Description copied from class: SnpSift

Show usage message

Specified by:

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

Overrides:

usage in class SnpSift