Package org.snpeff
Class SnpEff
- java.lang.Object
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- org.snpeff.SnpEff
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- 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
public class SnpEff extends java.lang.Object implements CommandLine
SnpEff's main command line program- Author:
- pcingola
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SnpEff.GeneDatabaseFormat
Available gene database formatsstatic class
SnpEff.InputFormat
Available input formatsstatic class
SnpEff.OutputFormat
Available output formats
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Field Summary
Fields Modifier and Type Field Description protected java.lang.String[]
args
static java.lang.String
BUILD
static java.lang.String
BUILD_DATE
protected boolean
canonical
protected java.lang.String
canonicalFile
protected java.lang.String
command
static int
COMMAND_LINE_WIDTH
protected Config
config
protected java.lang.String
configFile
protected java.util.Map<java.lang.String,java.lang.String>
configOverride
protected java.util.ArrayList<java.lang.String>
customIntervalFiles
protected java.lang.String
dataDir
protected boolean
debug
static java.lang.String
DEFAULT_COMMAND
protected boolean
download
protected boolean
expandIub
protected java.util.ArrayList<java.lang.String>
filterIntervalFiles
protected Genome
genome
protected java.lang.String
genomeVer
protected boolean
help
protected boolean
hgvs
protected boolean
hgvsForce
protected boolean
hgvsOld
protected boolean
hgvsOneLetterAa
protected boolean
hgvsShift
protected boolean
hgvsTrId
protected boolean
interaction
protected boolean
log
protected TranscriptSupportLevel
maxTranscriptSupportLevel
protected boolean
motif
protected boolean
multiThreaded
protected boolean
nextProt
protected boolean
nextProtKeepAllTrs
protected boolean
noGenome
protected int
numWorkers
protected boolean
onlyProtein
protected boolean
onlyRegulation
protected java.lang.String
onlyTranscriptsFile
protected java.lang.StringBuilder
output
protected boolean
quiet
protected java.util.HashSet<java.lang.String>
regulationTracks
static java.lang.String
REVISION
protected boolean
saveOutput
protected java.lang.String[]
shiftArgs
protected SnpEff
snpEffCmd
static java.lang.String
SOFTWARE_NAME
protected int
spliceRegionExonSize
protected int
spliceRegionIntronMax
protected int
spliceRegionIntronMin
protected int
spliceSiteSize
protected boolean
strict
protected boolean
suppressOutput
protected java.lang.Boolean
treatAllAsProteinCoding
protected int
upDownStreamLength
protected boolean
verbose
static java.lang.String
VERSION
static java.lang.String
VERSION_AUTHOR
static java.lang.String
VERSION_BUILD
static java.lang.String
VERSION_MAJOR
static java.lang.String
VERSION_SHORT
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addRegulationTrack(java.lang.String cellType)
protected void
canonical()
Filter canonical transcriptsSnpEff
cmd()
Create an appropriate SnpEffCmd* objectprotected java.lang.String
commandLineStr(boolean splitLines)
Command line argument list (try to fit it into COMMAND_LINE_WIDTH)void
error(java.lang.Throwable e, java.lang.String message)
Show an error (if not 'quiet' mode)void
fatalError(java.lang.String message)
Show an error message and exitjava.lang.String[]
getArgs()
Config
getConfig()
java.lang.String
getConfigFile()
java.lang.String
getOutput()
protected boolean
isOpt(java.lang.String arg)
Is this a command line option (e.g.void
load()
protected void
loadConfig()
Read config fileprotected int
loadCustomFile(java.lang.String fileName)
Read a custom interval filevoid
loadDb()
Load databaseprotected Markers
loadMarkers(java.lang.String fileName)
Read markers file Supported formats: BED, TXT, BigBed, GFFstatic void
main(java.lang.String[] args)
Mainvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsjava.util.HashMap<java.lang.String,java.lang.String>
reportValues()
Additional values to be reportedboolean
run()
Run according to command line optionsprotected boolean
run(SnpEff snpEff, java.lang.String[] args, java.lang.StringBuilder err)
Run a SnpEff (usually a sub-class)void
setCanonical(boolean canonical)
void
setConfig(Config config)
void
setConfigFile(java.lang.String configFile)
void
setDebug(boolean debug)
void
setGenomeVer(java.lang.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
setUpDownStreamLength(int upDownStreamLength)
void
setVerbose(boolean verbose)
void
usage(java.lang.String message)
Show 'usage' message and exit with an error code '-1'protected void
usageDb()
Show database load and build optionsprotected void
usageGeneric()
Show generic optionsprotected void
usageGenericAndDb()
static void
warning(java.lang.String warningType, java.lang.String details)
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Field Detail
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DEFAULT_COMMAND
public static final java.lang.String DEFAULT_COMMAND
- See Also:
- Constant Field Values
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COMMAND_LINE_WIDTH
public static final int COMMAND_LINE_WIDTH
- See Also:
- Constant Field Values
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SOFTWARE_NAME
public static final java.lang.String SOFTWARE_NAME
- See Also:
- Constant Field Values
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REVISION
public static final java.lang.String REVISION
- See Also:
- Constant Field Values
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BUILD
public static final java.lang.String BUILD
- See Also:
- Constant Field Values
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BUILD_DATE
public static final java.lang.String BUILD_DATE
- See Also:
- Constant Field Values
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VERSION_MAJOR
public static final java.lang.String VERSION_MAJOR
- See Also:
- Constant Field Values
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VERSION_SHORT
public static final java.lang.String VERSION_SHORT
- See Also:
- Constant Field Values
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VERSION_BUILD
public static final java.lang.String VERSION_BUILD
- See Also:
- Constant Field Values
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VERSION_AUTHOR
public static final java.lang.String VERSION_AUTHOR
- See Also:
- Constant Field Values
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VERSION
public static final java.lang.String VERSION
- See Also:
- Constant Field Values
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command
protected java.lang.String command
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args
protected java.lang.String[] args
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shiftArgs
protected java.lang.String[] shiftArgs
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canonical
protected boolean canonical
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debug
protected boolean debug
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download
protected boolean download
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expandIub
protected boolean expandIub
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help
protected boolean help
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hgvs
protected boolean hgvs
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hgvsForce
protected boolean hgvsForce
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hgvsOneLetterAa
protected boolean hgvsOneLetterAa
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hgvsOld
protected boolean hgvsOld
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hgvsShift
protected boolean hgvsShift
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hgvsTrId
protected boolean hgvsTrId
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interaction
protected boolean interaction
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log
protected boolean log
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motif
protected boolean motif
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multiThreaded
protected boolean multiThreaded
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nextProt
protected boolean nextProt
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nextProtKeepAllTrs
protected boolean nextProtKeepAllTrs
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noGenome
protected boolean noGenome
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onlyProtein
protected boolean onlyProtein
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onlyRegulation
protected boolean onlyRegulation
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quiet
protected boolean quiet
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strict
protected boolean strict
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saveOutput
protected boolean saveOutput
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suppressOutput
protected boolean suppressOutput
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verbose
protected boolean verbose
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treatAllAsProteinCoding
protected java.lang.Boolean treatAllAsProteinCoding
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numWorkers
protected int numWorkers
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spliceSiteSize
protected int spliceSiteSize
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spliceRegionExonSize
protected int spliceRegionExonSize
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spliceRegionIntronMin
protected int spliceRegionIntronMin
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spliceRegionIntronMax
protected int spliceRegionIntronMax
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upDownStreamLength
protected int upDownStreamLength
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configFile
protected java.lang.String configFile
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dataDir
protected java.lang.String dataDir
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genomeVer
protected java.lang.String genomeVer
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onlyTranscriptsFile
protected java.lang.String onlyTranscriptsFile
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canonicalFile
protected java.lang.String canonicalFile
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maxTranscriptSupportLevel
protected TranscriptSupportLevel maxTranscriptSupportLevel
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output
protected java.lang.StringBuilder output
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config
protected Config config
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genome
protected Genome genome
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snpEffCmd
protected SnpEff snpEffCmd
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customIntervalFiles
protected java.util.ArrayList<java.lang.String> customIntervalFiles
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filterIntervalFiles
protected java.util.ArrayList<java.lang.String> filterIntervalFiles
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regulationTracks
protected java.util.HashSet<java.lang.String> regulationTracks
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configOverride
protected java.util.Map<java.lang.String,java.lang.String> configOverride
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Method Detail
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main
public static void main(java.lang.String[] args)
Main
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warning
public static void warning(java.lang.String warningType, java.lang.String details)
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addRegulationTrack
public void addRegulationTrack(java.lang.String cellType)
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canonical
protected void canonical()
Filter canonical transcripts
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cmd
public SnpEff cmd()
Create an appropriate SnpEffCmd* object
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commandLineStr
protected java.lang.String commandLineStr(boolean splitLines)
Command line argument list (try to fit it into COMMAND_LINE_WIDTH)
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error
public void error(java.lang.Throwable e, java.lang.String message)
Show an error (if not 'quiet' mode)
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fatalError
public void fatalError(java.lang.String message)
Show an error message and exit
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getArgs
public java.lang.String[] getArgs()
- Specified by:
getArgs
in interfaceCommandLine
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getConfig
public Config getConfig()
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getConfigFile
public java.lang.String getConfigFile()
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getOutput
public java.lang.String getOutput()
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isOpt
protected boolean isOpt(java.lang.String arg)
Is this a command line option (e.g. "-tfam" is a command line option, but "-" means STDIN)
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load
public void load()
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loadConfig
protected void loadConfig()
Read config file
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loadCustomFile
protected int loadCustomFile(java.lang.String fileName)
Read a custom interval file
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loadDb
public void loadDb()
Load database
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loadMarkers
protected Markers loadMarkers(java.lang.String fileName)
Read markers file Supported formats: BED, TXT, BigBed, GFF
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
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reportValues
public java.util.HashMap<java.lang.String,java.lang.String> reportValues()
Additional values to be reported
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run
public boolean run()
Run according to command line options- Specified by:
run
in interfaceCommandLine
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run
protected boolean run(SnpEff snpEff, java.lang.String[] args, java.lang.StringBuilder err)
Run a SnpEff (usually a sub-class)
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setCanonical
public void setCanonical(boolean canonical)
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setConfig
public void setConfig(Config config)
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setConfigFile
public void setConfigFile(java.lang.String configFile)
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setDebug
public void setDebug(boolean debug)
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setGenomeVer
public void setGenomeVer(java.lang.String genomeVer)
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setLog
public void setLog(boolean log)
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setNextProt
public void setNextProt(boolean nextProt)
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setNextProtKeepAllTrs
public void setNextProtKeepAllTrs(boolean nextProtKeepAllTrs)
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setShiftHgvs
public void setShiftHgvs(boolean shiftHgvs)
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setSpliceSiteSize
public void setSpliceSiteSize(int spliceSiteSize)
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setSupressOutput
public void setSupressOutput(boolean suppressOutput)
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setUpDownStreamLength
public void setUpDownStreamLength(int upDownStreamLength)
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setVerbose
public void setVerbose(boolean verbose)
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usage
public void usage(java.lang.String message)
Show 'usage' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Parameters:
message
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usageDb
protected void usageDb()
Show database load and build options
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usageGeneric
protected void usageGeneric()
Show generic options
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usageGenericAndDb
protected void usageGenericAndDb()
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