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

      • 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)

      • 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

      • usageDb

        protected void usageDb()
        Show database load and build options

      • usageGeneric

        protected void usageGeneric()
        Show generic options

      • usageGenericAndDb

        protected void usageGenericAndDb()