Package org.snpsift

Class SnpSiftCmdAnnotate

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdAnnotate

All Implemented Interfaces:

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

public class SnpSiftCmdAnnotate
extends SnpSift

Annotate a VCF file with ID from another VCF file (database)

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
protected AnnotateVcfDb	annotateDb
protected boolean	annotateEmpty
protected java.lang.String	chrPrev
protected int	countBadRef
protected java.lang.String	existsInfoField
protected java.util.ArrayList<java.lang.String>	infoFields
protected int	maxBlockSize
protected org.snpsift.SnpSiftCmdAnnotate.AnnotationMethod	method
protected java.lang.String	prependInfoFieldName
static int	SHOW
protected boolean	useId
protected boolean	useInfoField
protected boolean	useRefAlt
protected org.snpeff.fileIterator.VcfFileIterator	vcfFile

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

Method Summary

Modifier and Type	Method	Description
boolean	annotate(org.snpeff.vcf.VcfEntry vcfEntry)
boolean	annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)	Initialize database for annotation process
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>	headers()	Build headers to add
void	init()	Initialize default values
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Annotate each entry of a VCF file
java.util.List<org.snpeff.vcf.VcfEntry>	run(boolean createList)	Run annotations
void	setAnnotateEmpty(boolean annotateEmpty)
void	usage(java.lang.String msg)	Show 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

SHOW

public static final int SHOW

See Also:

Constant Field Values

annotateEmpty

protected boolean annotateEmpty

useId

protected boolean useId

useInfoField

protected boolean useInfoField

useRefAlt

protected boolean useRefAlt

method

protected org.snpsift.SnpSiftCmdAnnotate.AnnotationMethod method

countBadRef

protected int countBadRef

maxBlockSize

protected int maxBlockSize

chrPrev

protected java.lang.String chrPrev

prependInfoFieldName

protected java.lang.String prependInfoFieldName

existsInfoField

protected java.lang.String existsInfoField

infoFields

protected java.util.ArrayList<java.lang.String> infoFields

vcfFile

protected org.snpeff.fileIterator.VcfFileIterator vcfFile

annotateDb

protected AnnotateVcfDb annotateDb

Constructor Detail

SnpSiftCmdAnnotate

public SnpSiftCmdAnnotate()

SnpSiftCmdAnnotate

public SnpSiftCmdAnnotate(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

annotateInit

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

Initialize database for annotation process

Specified by:

annotateInit in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotateInit in class SnpSift

headers

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

Build 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 arguments

Specified by:

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

Overrides:

parseArgs in class SnpSift

run

public boolean run()

Annotate each entry of a VCF file

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 annotations

Parameters:

createList - : If true, return a list with all annotated entries (used for test cases & debugging)

setAnnotateEmpty

public void setAnnotateEmpty(boolean annotateEmpty)

usage

public void usage(java.lang.String msg)

Show usage message

Specified by:

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

Overrides:

usage in class SnpSift