Package org.snpsift
Class SnpSift
java.lang.Object
org.snpsift.SnpSift
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
- Direct Known Subclasses:
SnpSiftCmdAlleleMatrix
,SnpSiftCmdAnnotate
,SnpSiftCmdCaseControl
,SnpSiftCmdCaseControlSummary
,SnpSiftCmdConcordance
,SnpSiftCmdCovarianceMatrix
,SnpSiftCmdDbNsfp
,SnpSiftCmdExtractFields
,SnpSiftCmdFilter
,SnpSiftCmdFilterChrPos
,SnpSiftCmdFilterGt
,SnpSiftCmdGeneSets
,SnpSiftCmdGt
,SnpSiftCmdGwasCatalog
,SnpSiftCmdHwe
,SnpSiftCmdIntersect
,SnpSiftCmdIntervals
,SnpSiftCmdIntervalsIndex
,SnpSiftCmdJoin
,SnpSiftCmdPedShow
,SnpSiftCmdPhastCons
,SnpSiftCmdPrivate
,SnpSiftCmdRemoveReferenceGenotypes
,SnpSiftCmdRmInfo
,SnpSiftCmdSort
,SnpSiftCmdSplit
,SnpSiftCmdTsTv
,SnpSiftCmdVarType
,SnpSiftCmdVcf2Tped
,SnpSiftCmdVcfCheck
,SnpSiftCmdVcfOperator
public class SnpSift
extends Object
implements org.snpeff.snpEffect.VcfAnnotator, org.snpeff.snpEffect.commandLine.CommandLine
Generic SnpSift tool caller
- Author:
- pablocingolani
-
Field Summary
FieldsModifier and TypeFieldDescriptionprotected String[]
static final String
protected String
protected org.snpeff.snpEffect.Config
protected String
protected String
protected String
protected boolean
protected String
protected boolean
protected boolean
static final String[]
protected String
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected int
protected StringBuilder
protected boolean
static final String
protected boolean
protected String[]
static int
protected boolean
protected boolean
static final String
protected boolean
protected boolean
protected boolean
protected String
protected boolean
static final String
static final String
static final String
static final String
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
addHeaders
(org.snpeff.fileIterator.VcfFileIterator vcfFile) Add VCF headersboolean
annotate
(org.snpeff.vcf.VcfEntry vcfEntry) boolean
annotateFinish
(org.snpeff.fileIterator.VcfFileIterator vcfFile) boolean
annotateInit
(org.snpeff.fileIterator.VcfFileIterator vcfFile) cmd()
Run: Executes the appropriate classprotected String
Show command lineprotected boolean
Download a databaseprotected String
Find database file name.void
Show an error (if not 'quiet' mode)String[]
getArgs()
org.snpeff.snpEffect.Config
protected List
<org.snpeff.vcf.VcfHeaderEntry> headers()
Headers to addvoid
init()
Initialize default valuesprotected boolean
Is this a command line option (e.g.protected void
Read config filestatic void
Mainprotected org.snpeff.fileIterator.VcfFileIterator
Open VCF input filevoid
Parse command line argumentsprotected String
processVcfHeader
(org.snpeff.fileIterator.VcfFileIterator vcf) Process VCF header related issuesboolean
run()
void
setCommand
(Class clss) void
setCommand
(String command) void
setConfig
(org.snpeff.snpEffect.Config config) void
setConfigFile
(String configFile) void
setDbFileName
(String dbFileName) void
setDebug
(boolean debug) void
setQuiet
(boolean quiet) void
setSaveOutput
(boolean saveOutput) void
setShowVcfHeader
(boolean showVcfHeader) void
setShowVersion
(boolean showVersion) void
setSuppressOutput
(boolean suppressOutput) void
setVcfHeaderAddProgramVersion
(boolean vcfHeaderAddProgramVersion) void
setVerbose
(boolean verbose) void
showCmd()
Show command linevoid
Show version numberunSanitize
(String str) Convert a sanitized expression (from Galaxy) back to the original string References: http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg00530.htmlvoid
Show usage messageprotected void
Options common to all commands
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Field Details
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BUILD
- See Also:
-
SOFTWARE_NAME
- See Also:
-
VERSION_MAJOR
- See Also:
-
REVISION
- See Also:
-
VERSION_SHORT
- See Also:
-
VERSION
- See Also:
-
VERSION_NO_NAME
- See Also:
-
SHOW_EVERY_VCFLINES
public static int SHOW_EVERY_VCFLINES -
EMPTY_ARGS
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dbTabix
protected boolean dbTabix -
debug
protected boolean debug -
download
protected boolean download -
help
protected boolean help -
log
protected boolean log -
needsConfig
protected boolean needsConfig -
needsDb
protected boolean needsDb -
needsGenome
protected boolean needsGenome -
quiet
protected boolean quiet -
saveOutput
protected boolean saveOutput -
showVcfHeader
protected boolean showVcfHeader -
showVersion
protected boolean showVersion -
suppressOutput
protected boolean suppressOutput -
vcfHeaderProcessed
protected boolean vcfHeaderProcessed -
vcfHeaderAddProgramVersion
protected boolean vcfHeaderAddProgramVersion -
verbose
protected boolean verbose -
args
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command
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dbFileName
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dbType
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genomeVersion
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vcfInputFile
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numWorkers
protected int numWorkers -
output
-
errCount
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config
protected org.snpeff.snpEffect.Config config -
configFile
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dataDir
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shiftArgs
-
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Constructor Details
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SnpSift
public SnpSift() -
SnpSift
-
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Method Details
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main
Main -
addHeaders
public boolean addHeaders(org.snpeff.fileIterator.VcfFileIterator vcfFile) Add VCF headers- Specified by:
addHeaders
in interfaceorg.snpeff.snpEffect.VcfAnnotator
-
annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry) - Specified by:
annotate
in interfaceorg.snpeff.snpEffect.VcfAnnotator
-
annotateFinish
public boolean annotateFinish(org.snpeff.fileIterator.VcfFileIterator vcfFile) - Specified by:
annotateFinish
in interfaceorg.snpeff.snpEffect.VcfAnnotator
-
annotateInit
public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile) - Specified by:
annotateInit
in interfaceorg.snpeff.snpEffect.VcfAnnotator
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cmd
Run: Executes the appropriate class -
commandLineStr
Show command line -
databaseDownload
protected boolean databaseDownload()Download a database -
databaseFind
Find database file name. -
error
Show an error (if not 'quiet' mode) -
getArgs
- Specified by:
getArgs
in interfaceorg.snpeff.snpEffect.commandLine.CommandLine
-
getConfig
public org.snpeff.snpEffect.Config getConfig() -
getConfigFile
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getOutput
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headers
Headers to add -
init
public void init()Initialize default values -
isOpt
Is this a command line option (e.g. "-tfam" is a command line option, but "-" means STDIN) -
loadConfig
protected void loadConfig()Read config file -
openVcfInputFile
protected org.snpeff.fileIterator.VcfFileIterator openVcfInputFile()Open VCF input file -
parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceorg.snpeff.snpEffect.commandLine.CommandLine
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processVcfHeader
Process VCF header related issues -
run
public boolean run()- Specified by:
run
in interfaceorg.snpeff.snpEffect.commandLine.CommandLine
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setCommand
-
setCommand
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setConfig
public void setConfig(org.snpeff.snpEffect.Config config) - Specified by:
setConfig
in interfaceorg.snpeff.snpEffect.VcfAnnotator
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setConfigFile
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setDbFileName
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setDebug
public void setDebug(boolean debug) - Specified by:
setDebug
in interfaceorg.snpeff.snpEffect.VcfAnnotator
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setQuiet
public void setQuiet(boolean quiet) -
setSaveOutput
public void setSaveOutput(boolean saveOutput) -
setShowVcfHeader
public void setShowVcfHeader(boolean showVcfHeader) -
setShowVersion
public void setShowVersion(boolean showVersion) -
setSuppressOutput
public void setSuppressOutput(boolean suppressOutput) -
setVcfHeaderAddProgramVersion
public void setVcfHeaderAddProgramVersion(boolean vcfHeaderAddProgramVersion) -
setVerbose
public void setVerbose(boolean verbose) - Specified by:
setVerbose
in interfaceorg.snpeff.snpEffect.VcfAnnotator
-
showCmd
public void showCmd()Show command line -
showVersion
public void showVersion()Show version number -
unSanitize
Convert a sanitized expression (from Galaxy) back to the original string References: http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg00530.html -
usage
Show usage message- Specified by:
usage
in interfaceorg.snpeff.snpEffect.commandLine.CommandLine
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usageGenericAndDb
protected void usageGenericAndDb()Options common to all commands
-