Package org.snpeff.snpEffect

Class Config

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Iterable<java.lang.String>
    public class Config
extends java.lang.Object
implements java.io.Serializable, java.lang.Iterable<java.lang.String>
    See Also:
    Serialized Form

    • Field Detail

      • DEFAULT_CONFIG_FILE

        public static final java.lang.String DEFAULT_CONFIG_FILE
        See Also:
        Constant Field Values

      • PREFERRED_CONFIG_FILE

        public static final java.lang.String PREFERRED_CONFIG_FILE

      • DEFAULT_DATA_DIR

        public static final java.lang.String DEFAULT_DATA_DIR
        See Also:
        Constant Field Values

      • KEY_BUNDLE_SUFIX

        public static final java.lang.String KEY_BUNDLE_SUFIX
        See Also:
        Constant Field Values

      • KEY_CODON_PREFIX

        public static final java.lang.String KEY_CODON_PREFIX
        See Also:
        Constant Field Values

      • KEY_CODONTABLE_SUFIX

        public static final java.lang.String KEY_CODONTABLE_SUFIX
        See Also:
        Constant Field Values

      • KEY_DATABASE_LOCAL

        public static final java.lang.String KEY_DATABASE_LOCAL
        See Also:
        Constant Field Values

      • KEY_DATABASE_REPOSITORY

        public static final java.lang.String KEY_DATABASE_REPOSITORY
        See Also:
        Constant Field Values

      • KEY_DATABASE_REPOSITORY_KEY

        public static final java.lang.String KEY_DATABASE_REPOSITORY_KEY
        See Also:
        Constant Field Values

      • KEY_DBNSFP_FIELDS

        public static final java.lang.String KEY_DBNSFP_FIELDS
        See Also:
        Constant Field Values

      • KEY_GENOME_SUFIX

        public static final java.lang.String KEY_GENOME_SUFIX
        See Also:
        Constant Field Values

      • KEY_LOF_IGNORE_PROTEIN_CODING_AFTER

        public static final java.lang.String KEY_LOF_IGNORE_PROTEIN_CODING_AFTER
        See Also:
        Constant Field Values

      • KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE

        public static final java.lang.String KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE
        See Also:
        Constant Field Values

      • KEY_LOF_DELETE_PROTEIN_CODING_BASES

        public static final java.lang.String KEY_LOF_DELETE_PROTEIN_CODING_BASES
        See Also:
        Constant Field Values

      • KEY_REFERENCE_SUFIX

        public static final java.lang.String KEY_REFERENCE_SUFIX
        See Also:
        Constant Field Values

      • KEY_VERSIONS_URL

        public static final java.lang.String KEY_VERSIONS_URL
        See Also:
        Constant Field Values

      • COMPATIBLE_WITH_5_1

        public static final java.lang.String[] COMPATIBLE_WITH_5_1

      • DATABASE_COMPATIBLE_VERSIONS

        public static final java.util.Map<java.lang.String,​java.lang.String[]> DATABASE_COMPATIBLE_VERSIONS

      • GENOMES_DIR

        public static java.lang.String GENOMES_DIR

      • DEFAULT_COORDINATES

        public static java.lang.String DEFAULT_COORDINATES

    • Constructor Detail

      • Config

        public Config​(Genome genome)
        This constructor is used in test cases

      • Config

        public Config​(java.lang.String genomeVersion)
        Create a config (uses DEFAULT_CONFIG_FILE)

      • Config

        public Config​(java.lang.String genomeVersion,
              java.lang.String configFileName)
        Create a configuration from 'configFileName'

      • Config

        public Config​(java.lang.String genomeVersion,
              java.lang.String configFileName,
              java.lang.String dataDir,
              java.util.Map<java.lang.String,​java.lang.String> override)
        Create a configuration from 'configFileName'

      • Config

        public Config​(java.lang.String genomeVersion,
              java.lang.String configFileName,
              java.lang.String dataDir,
              java.util.Map<java.lang.String,​java.lang.String> override,
              boolean verbose)

    • Method Detail

      • get

        public static Config get()

      • reset

        public static Config reset()

      • defaultConfigFile

        public static java.lang.String defaultConfigFile()
        If Debian-preferred config file is available, give it. else, if the config file in /etc/snpeff is available, give it. Else, default to DEFAULT_CONFIG_FILE.

      • downloadUrl

        public java.util.List<java.net.URL> downloadUrl​(java.lang.String genomeVer)
        Get a list of URLs that can be used to download a database Use compatible versions from 'getDatabaseCompatibilityVersions()'

      • downloadUrl

        public java.net.URL downloadUrl​(java.lang.String genomeVer,
                                java.lang.String version)
        Build the URL for downloading a database file

        Format : DatabaseRepository / v VERSION / snpEff_v VERSION _ genomeVersion .zip Example : http://downloads.sourceforge.net/project/snpeff/databases/v2_0_3/snpEff_v2_0_3_EF3.64.zip

      • getBaseFileNameGenes

        public java.lang.String getBaseFileNameGenes()
        Genes file path (no extension)

      • getBaseFileNameMotif

        public java.lang.String getBaseFileNameMotif()

      • getBaseFileNameRegulation

        public java.lang.String getBaseFileNameRegulation()
        Regulation file (GFF format)

      • getBaseFileNameSequence

        public java.lang.String getBaseFileNameSequence()

      • getBundleName

        public java.lang.String getBundleName​(java.lang.String genomeVer)
        Is this genome packed in a bundle?

      • getConfigFileName

        public java.lang.String getConfigFileName()

      • getCoordinates

        public java.lang.String getCoordinates()

      • getDatabaseCompatibilityVersions

        public java.util.List<java.lang.String> getDatabaseCompatibilityVersions()
        Return a list of databases that are compatible with this SnpEff version number

      • getDatabaseLocal

        public java.lang.String getDatabaseLocal​(java.lang.String dbName)
        Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.

      • getDatabaseLocalKey

        public java.lang.String getDatabaseLocalKey​(java.lang.String dbName)

      • getDatabaseRepository

        public java.lang.String getDatabaseRepository()

      • getDatabaseRepository

        public java.lang.String getDatabaseRepository​(java.lang.String dbName)
        Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.

      • getDatabaseRepositoryUrl

        public java.net.URL getDatabaseRepositoryUrl​(java.lang.String dbName)

      • getDbNsfpFields

        public java.lang.String getDbNsfpFields()

      • getDirData

        public java.lang.String getDirData()
        Main data directory

      • getDirDataGenomeVersion

        public java.lang.String getDirDataGenomeVersion()
        Data dir for a specific genome version (i.e. where the database is)

      • getDirMain

        public java.lang.String getDirMain()
        Main dir

      • getDirRegulationBed

        public java.lang.String getDirRegulationBed()
        Directory where regulation 'BED' files are

      • getDouble

        public double getDouble​(java.lang.String propertyName,
                        double defaultValue)
        Get a property as a double

      • getFileListGenomeFasta

        public java.util.List<java.lang.String> getFileListGenomeFasta()
        Filenames for reference sequence (fasta files)

      • getFileNameCds

        public java.lang.String getFileNameCds()

      • getFileNameGenomeFasta

        public java.lang.String getFileNameGenomeFasta()
        Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that exists

      • getFileNameProteins

        public java.lang.String getFileNameProteins()

      • getFileNameSequence

        public java.lang.String getFileNameSequence()

      • getFileNameSequence

        public java.lang.String getFileNameSequence​(java.lang.String chr)

      • getFileSnpEffectPredictor

        public java.lang.String getFileSnpEffectPredictor()

      • getGenome

        public Genome getGenome()

      • getGenome

        public Genome getGenome​(java.lang.String genomeId)

      • getGenomeVersion

        public java.lang.String getGenomeVersion()

      • getLofDeleteProteinCodingBases

        public double getLofDeleteProteinCodingBases()

      • getLofIgnoreProteinCodingAfter

        public double getLofIgnoreProteinCodingAfter()

      • getLofIgnoreProteinCodingBefore

        public double getLofIgnoreProteinCodingBefore()

      • getLong

        public long getLong​(java.lang.String propertyName,
                    long defaultValue)
        Get a property as a long

      • getName

        public java.lang.String getName​(java.lang.String genomeVersion)

      • getReference

        public java.lang.String getReference​(java.lang.String genomeVersion)

      • setSnpEffectPredictor

        public void setSnpEffectPredictor​(SnpEffectPredictor snpEffectPredictor)

      • getString

        public java.lang.String getString​(java.lang.String propertyName)
        Get a property as a string

      • getString

        public java.lang.String getString​(java.lang.String propertyName,
                                  java.lang.String defaultValue)
        Get a property as a string

      • getVersionsUrl

        public java.lang.String getVersionsUrl()

      • isDebug

        public boolean isDebug()

      • setDebug

        public void setDebug​(boolean debug)

      • isErrorChromoHit

        public boolean isErrorChromoHit()

      • setErrorChromoHit

        public void setErrorChromoHit​(boolean errorChromoHit)

      • isErrorOnMissingChromo

        public boolean isErrorOnMissingChromo()

      • setErrorOnMissingChromo

        public void setErrorOnMissingChromo​(boolean errorOnMissingChromo)

      • isExpandIub

        public boolean isExpandIub()

      • setExpandIub

        public void setExpandIub​(boolean expandIub)

      • isHgvs

        public boolean isHgvs()

      • isHgvs1LetterAA

        public boolean isHgvs1LetterAA()

      • isHgvsOld

        public boolean isHgvsOld()

      • setHgvsOld

        public void setHgvsOld​(boolean hgvsDnaOld)

      • isHgvsShift

        public boolean isHgvsShift()

      • setHgvsShift

        public void setHgvsShift​(boolean hgvsShift)

      • isHgvsTrId

        public boolean isHgvsTrId()

      • setHgvsTrId

        public void setHgvsTrId​(boolean hgvsTrId)

      • isOnlyRegulation

        public boolean isOnlyRegulation()

      • setOnlyRegulation

        public void setOnlyRegulation​(boolean onlyRegulation)

      • isQuiet

        public boolean isQuiet()

      • setQuiet

        public void setQuiet​(boolean quiet)

      • isTreatAllAsProteinCoding

        public boolean isTreatAllAsProteinCoding()

      • setTreatAllAsProteinCoding

        public void setTreatAllAsProteinCoding​(boolean treatAllAsProteinCoding)

      • isVerbose

        public boolean isVerbose()

      • setVerbose

        public void setVerbose​(boolean verbose)

      • iterator

        public java.util.Iterator<java.lang.String> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<java.lang.String>

      • keys

        public java.util.List<java.lang.String> keys()

      • loadSnpEffectPredictor

        public SnpEffectPredictor loadSnpEffectPredictor()
        Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)

      • setHgvsOneLetterAA

        public void setHgvsOneLetterAA​(boolean hgvsOneLetterAa)

      • setString

        public void setString​(java.lang.String propertyName,
                      java.lang.String value)

      • setUseHgvs

        public void setUseHgvs​(boolean useHgvs)

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object