Package org.snpeff

Class SnpEff

    • Field Detail

      • command

        protected java.lang.String command
      • args

        protected java.lang.String[] args
      • shiftArgs

        protected java.lang.String[] shiftArgs
      • 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
      • verbose

        protected boolean verbose
      • treatAllAsProteinCoding

        protected java.lang.Boolean treatAllAsProteinCoding
      • 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

        protected java.lang.String configFile
      • dataDir

        protected java.lang.String dataDir
      • genomeVer

        protected java.lang.String genomeVer
      • onlyTranscriptsFile

        protected java.lang.String onlyTranscriptsFile
      • canonicalFile

        protected java.lang.String canonicalFile
      • output

        protected java.lang.StringBuilder output
      • config

        protected Config config
      • genome

        protected Genome genome
      • snpEffCmd

        protected SnpEff snpEffCmd
      • customIntervalFiles

        protected java.util.ArrayList<java.lang.String> customIntervalFiles
      • filterIntervalFiles

        protected java.util.ArrayList<java.lang.String> filterIntervalFiles
      • regulationTracks

        protected java.util.HashSet<java.lang.String> regulationTracks
      • configOverride

        protected java.util.Map<java.lang.String,​java.lang.String> configOverride
    • Constructor Detail

      • SnpEff

        public SnpEff()
      • SnpEff

        public SnpEff​(java.lang.String[] args)
    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
        Main
      • warning

        public static void warning​(java.lang.String warningType,
                                   java.lang.String details)
      • addRegulationTrack

        public void addRegulationTrack​(java.lang.String cellType)
      • canonical

        protected void canonical()
        Filter canonical transcripts
      • cmd

        public SnpEff cmd()
        Create an appropriate SnpEffCmd* object
      • commandLineStr

        protected java.lang.String commandLineStr​(boolean splitLines)
        Command line argument list (try to fit it into COMMAND_LINE_WIDTH)
      • error

        public void error​(java.lang.Throwable e,
                          java.lang.String message)
        Show an error (if not 'quiet' mode)
      • fatalError

        public void fatalError​(java.lang.String message)
        Show an error message and exit
      • getArgs

        public java.lang.String[] getArgs()
        Specified by:
        getArgs in interface CommandLine
      • getConfig

        public Config getConfig()
      • getConfigFile

        public java.lang.String getConfigFile()
      • getOutput

        public java.lang.String getOutput()
      • 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)
      • load

        public void load()
      • loadConfig

        protected void loadConfig()
        Read config file
      • loadCustomFile

        protected int loadCustomFile​(java.lang.String fileName)
        Read a custom interval file
      • loadDb

        public void loadDb()
        Load database
      • loadMarkers

        protected Markers loadMarkers​(java.lang.String fileName)
        Read markers file Supported formats: BED, TXT, BigBed, GFF
      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Parse command line arguments
        Specified by:
        parseArgs in interface CommandLine
      • reportValues

        public java.util.HashMap<java.lang.String,​java.lang.String> reportValues()
        Additional values to be reported
      • run

        public boolean run()
        Run according to command line options
        Specified by:
        run in interface CommandLine
      • run

        protected boolean run​(SnpEff snpEff,
                              java.lang.String[] args,
                              java.lang.StringBuilder err)
        Run a SnpEff (usually a sub-class)
      • setCanonical

        public void setCanonical​(boolean canonical)
      • setConfig

        public void setConfig​(Config config)
      • setConfigFile

        public void setConfigFile​(java.lang.String configFile)
      • setDebug

        public void setDebug​(boolean debug)
      • setGenomeVer

        public void setGenomeVer​(java.lang.String genomeVer)
      • 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)
      • setUpDownStreamLength

        public void setUpDownStreamLength​(int upDownStreamLength)
      • setVerbose

        public void setVerbose​(boolean verbose)
      • usage

        public void usage​(java.lang.String message)
        Show 'usage' message and exit with an error code '-1'
        Specified by:
        usage in interface CommandLine
        Parameters:
        message -
      • usageDb

        protected void usageDb()
        Show database load and build options
      • usageGeneric

        protected void usageGeneric()
        Show generic options
      • usageGenericAndDb

        protected void usageGenericAndDb()