Package org.snpsift

Class SnpSift

    • Field Detail

      • SHOW_EVERY_VCFLINES

        public static int SHOW_EVERY_VCFLINES
      • EMPTY_ARGS

        public static final java.lang.String[] EMPTY_ARGS
      • 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

        protected java.lang.String[] args
      • command

        protected java.lang.String command
      • dbFileName

        protected java.lang.String dbFileName
      • dbType

        protected java.lang.String dbType
      • genomeVersion

        protected java.lang.String genomeVersion
      • vcfInputFile

        protected java.lang.String vcfInputFile
      • numWorkers

        protected int numWorkers
      • output

        protected java.lang.StringBuilder output
      • errCount

        protected java.util.HashMap<java.lang.String,​java.lang.Integer> errCount
      • config

        protected org.snpeff.snpEffect.Config config
      • configFile

        protected java.lang.String configFile
      • dataDir

        protected java.lang.String dataDir
      • shiftArgs

        protected java.lang.String[] shiftArgs
    • Constructor Detail

      • SnpSift

        public SnpSift()
      • SnpSift

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

      • main

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

        public boolean addHeaders​(org.snpeff.fileIterator.VcfFileIterator vcfFile)
        Add VCF headers
        Specified by:
        addHeaders in interface org.snpeff.snpEffect.VcfAnnotator
      • annotate

        public boolean annotate​(org.snpeff.vcf.VcfEntry vcfEntry)
        Specified by:
        annotate in interface org.snpeff.snpEffect.VcfAnnotator
      • annotateFinish

        public boolean annotateFinish​(org.snpeff.fileIterator.VcfFileIterator vcfFile)
        Specified by:
        annotateFinish in interface org.snpeff.snpEffect.VcfAnnotator
      • annotateInit

        public boolean annotateInit​(org.snpeff.fileIterator.VcfFileIterator vcfFile)
        Specified by:
        annotateInit in interface org.snpeff.snpEffect.VcfAnnotator
      • cmd

        public SnpSift cmd()
        Run: Executes the appropriate class
      • commandLineStr

        protected java.lang.String commandLineStr()
        Show command line
      • databaseDownload

        protected boolean databaseDownload()
        Download a database
      • databaseFind

        protected java.lang.String databaseFind()
        Find database file name.
      • error

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

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

        public org.snpeff.snpEffect.Config getConfig()
      • getConfigFile

        public java.lang.String getConfigFile()
      • getOutput

        public java.lang.String getOutput()
      • headers

        protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
        Headers to add
      • init

        public void init()
        Initialize default values
      • 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)
      • loadConfig

        protected void loadConfig()
        Read config file
      • openVcfInputFile

        protected org.snpeff.fileIterator.VcfFileIterator openVcfInputFile()
        Open VCF input file
      • parseArgs

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

        protected java.lang.String processVcfHeader​(org.snpeff.fileIterator.VcfFileIterator vcf)
        Process VCF header related issues
      • run

        public boolean run()
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
      • setCommand

        public void setCommand​(java.lang.Class clss)
      • setCommand

        public void setCommand​(java.lang.String command)
      • setConfig

        public void setConfig​(org.snpeff.snpEffect.Config config)
        Specified by:
        setConfig in interface org.snpeff.snpEffect.VcfAnnotator
      • setConfigFile

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

        public void setDbFileName​(java.lang.String dbFileName)
      • setDebug

        public void setDebug​(boolean debug)
        Specified by:
        setDebug in interface org.snpeff.snpEffect.VcfAnnotator
      • 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 interface org.snpeff.snpEffect.VcfAnnotator
      • showCmd

        public void showCmd()
        Show command line
      • showVersion

        public void showVersion()
        Show version number
      • unSanitize

        public java.lang.String unSanitize​(java.lang.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.html
      • usage

        public void usage​(java.lang.String msg)
        Show usage message
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
      • usageGenericAndDb

        protected void usageGenericAndDb()
        Options common to all commands