Package org.snpeff
Class SnpEff
java.lang.Object
org.snpeff.SnpEff
- All Implemented Interfaces:
CommandLine
- Direct Known Subclasses:
SnpEffCmdAcat
,SnpEffCmdBuild
,SnpEffCmdBuildNextProt
,SnpEffCmdCds
,SnpEffCmdClosest
,SnpEffCmdCount
,SnpEffCmdDatabases
,SnpEffCmdDownload
,SnpEffCmdDump
,SnpEffCmdEff
,SnpEffCmdGenes2Bed
,SnpEffCmdGsa
,SnpEffCmdLen
,SnpEffCmdPdb
,SnpEffCmdProtein
,SnpEffCmdSeq
,SnpEffCmdShow
,SnpEffCmdSpliceAnalysis
,SnpEffCmdTranslocationsReport
SnpEff's main command line program
- Author:
- pcingola
-
Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic enum
Available gene database formatsstatic enum
Available input formatsstatic enum
Available output formats -
Field Summary
FieldsModifier and TypeFieldDescriptionprotected String[]
static final String
static final String
protected boolean
protected String
protected String
static final int
protected Config
protected String
protected String
protected boolean
static final String
protected boolean
protected boolean
protected Genome
protected String
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected TranscriptSupportLevel
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected int
protected boolean
protected boolean
protected String
protected StringBuilder
protected boolean
static final String
protected boolean
protected String[]
protected SnpEff
static final String
protected int
protected int
protected int
protected int
protected boolean
protected boolean
protected boolean
protected Boolean
protected int
protected boolean
static final String
static final String
static final String
static final String
static final String
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addRegulationTrack
(String cellType) protected void
Filter canonical transcriptscmd()
Create an appropriate SnpEffCmd* objectprotected String
commandLineStr
(boolean splitLines) Command line argument list (try to fit it into COMMAND_LINE_WIDTH)protected void
Filter by tagsString[]
getArgs()
protected boolean
Is this a command line option (e.g.void
load()
protected void
Read config fileprotected int
loadCustomFile
(String fileName) Read a custom interval filevoid
loadDb()
Load databaseprotected Markers
loadMarkers
(String fileName) Read markers file Supported formats: BED, TXT, BigBed, GFFstatic void
Mainvoid
Parse command line argumentsAdditional values to be reportedboolean
run()
Run according to command line optionsprotected boolean
run
(SnpEff snpEff, String[] args, StringBuilder err) Run a SnpEff (usually a sub-class)void
setCanonical
(boolean canonical) void
void
setConfigFile
(String configFile) void
setDebug
(boolean debug) void
setGenomeVer
(String genomeVer) void
setLog
(boolean log) void
setNextProt
(boolean nextProt) void
setNextProtKeepAllTrs
(boolean nextProtKeepAllTrs) void
setShiftHgvs
(boolean shiftHgvs) void
setSpliceSiteSize
(int spliceSiteSize) void
setSupressOutput
(boolean suppressOutput) void
setTesting
(boolean testing) void
setUpDownStreamLength
(int upDownStreamLength) void
setVerbose
(boolean verbose) void
Show 'usage' message and exit with an error code '-1'protected void
usageDb()
Show database load and build optionsprotected void
Show generic optionsprotected void
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Field Details
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DEFAULT_COMMAND
- See Also:
-
COMMAND_LINE_WIDTH
public static final int COMMAND_LINE_WIDTH- See Also:
-
SOFTWARE_NAME
- See Also:
-
REVISION
- See Also:
-
BUILD
- See Also:
-
BUILD_DATE
- See Also:
-
VERSION_MAJOR
- See Also:
-
VERSION_SHORT
- See Also:
-
VERSION_BUILD
- See Also:
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VERSION_AUTHOR
- See Also:
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VERSION
- See Also:
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command
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args
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shiftArgs
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canonical
protected boolean canonical -
debug
protected boolean debug -
download
protected boolean download -
expandIub
protected boolean expandIub -
help
protected boolean help -
hgvs
protected boolean hgvs -
hgvsForce
protected boolean hgvsForce -
hgvsOneLetterAa
protected boolean hgvsOneLetterAa -
hgvsOld
protected boolean hgvsOld -
hgvsShift
protected boolean hgvsShift -
hgvsTrId
protected boolean hgvsTrId -
interaction
protected boolean interaction -
log
protected boolean log -
motif
protected boolean motif -
multiThreaded
protected boolean multiThreaded -
nextProt
protected boolean nextProt -
nextProtKeepAllTrs
protected boolean nextProtKeepAllTrs -
noGenome
protected boolean noGenome -
onlyProtein
protected boolean onlyProtein -
onlyRegulation
protected boolean onlyRegulation -
quiet
protected boolean quiet -
strict
protected boolean strict -
saveOutput
protected boolean saveOutput -
suppressOutput
protected boolean suppressOutput -
testing
protected boolean testing -
verbose
protected boolean verbose -
treatAllAsProteinCoding
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numWorkers
protected int numWorkers -
spliceSiteSize
protected int spliceSiteSize -
spliceRegionExonSize
protected int spliceRegionExonSize -
spliceRegionIntronMin
protected int spliceRegionIntronMin -
spliceRegionIntronMax
protected int spliceRegionIntronMax -
upDownStreamLength
protected int upDownStreamLength -
configFile
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dataDir
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genomeVer
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onlyTranscriptsFile
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canonicalFile
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tags
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tagsNo
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maxTranscriptSupportLevel
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output
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config
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genome
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snpEffCmd
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customIntervalFiles
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filterIntervalFiles
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regulationTracks
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configOverride
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Constructor Details
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SnpEff
public SnpEff() -
SnpEff
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Method Details
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main
Main -
addRegulationTrack
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canonical
protected void canonical()Filter canonical transcripts -
cmd
Create an appropriate SnpEffCmd* object -
commandLineStr
Command line argument list (try to fit it into COMMAND_LINE_WIDTH) -
filterTags
protected void filterTags()Filter by tags -
getArgs
- Specified by:
getArgs
in interfaceCommandLine
-
getConfig
-
getConfigFile
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getOutput
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isOpt
Is this a command line option (e.g. "-tfam" is a command line option, but "-" means STDIN) -
load
public void load() -
loadConfig
protected void loadConfig()Read config file -
loadCustomFile
Read a custom interval file -
loadDb
public void loadDb()Load database -
loadMarkers
Read markers file Supported formats: BED, TXT, BigBed, GFF -
parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
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reportValues
Additional values to be reported -
run
public boolean run()Run according to command line options- Specified by:
run
in interfaceCommandLine
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run
Run a SnpEff (usually a sub-class) -
setCanonical
public void setCanonical(boolean canonical) -
setConfig
-
setConfigFile
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setDebug
public void setDebug(boolean debug) -
setGenomeVer
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setLog
public void setLog(boolean log) -
setNextProt
public void setNextProt(boolean nextProt) -
setNextProtKeepAllTrs
public void setNextProtKeepAllTrs(boolean nextProtKeepAllTrs) -
setShiftHgvs
public void setShiftHgvs(boolean shiftHgvs) -
setSpliceSiteSize
public void setSpliceSiteSize(int spliceSiteSize) -
setSupressOutput
public void setSupressOutput(boolean suppressOutput) -
setTesting
public void setTesting(boolean testing) -
setUpDownStreamLength
public void setUpDownStreamLength(int upDownStreamLength) -
setVerbose
public void setVerbose(boolean verbose) -
usage
Show 'usage' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
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usageDb
protected void usageDb()Show database load and build options -
usageGeneric
protected void usageGeneric()Show generic options -
usageGenericAndDb
protected void usageGenericAndDb()
-