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