Package org.snpeff.snpEffect
Class Config
java.lang.Object
org.snpeff.snpEffect.Config
- All Implemented Interfaces:
Serializable
,Iterable<String>
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String[]
static final String[]
static final String
static String
static final String
static final String
static String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
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Constructor Summary
ConstructorsConstructorDescriptionCreate a config (uses DEFAULT_CONFIG_FILE)Create a configuration from 'configFileName'Create a configuration from 'configFileName'Config
(String genomeVersion, String configFileName, String dataDir, Map<String, String> override, boolean verbose) This constructor is used in test cases -
Method Summary
Modifier and TypeMethodDescriptionstatic String
If Debian-preferred config file is available, give it.downloadUrl
(String genomeVer) Get a list of URLs that can be used to download a database Use compatible versions from 'getDatabaseCompatibilityVersions()'downloadUrl
(String genomeVer, String version) Build the URL for downloading a database filestatic Config
get()
Genes file path (no extension)Regulation file (GFF format)getBundleName
(String genomeVer) Is this genome packed in a bundle?Return a list of databases that are compatible with this SnpEff version numbergetDatabaseLocal
(String dbName) Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.getDatabaseLocalKey
(String dbName) getDatabaseRepository
(String dbName) Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.getDatabaseRepositoryUrl
(String dbName) Main data directoryData dir for a specific genome version (i.e.Main dirDirectory where regulation 'BED' files aredouble
Get a property as a doubleFilenames for reference sequence (fasta files)Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that existsdouble
double
double
long
Get a property as a longgetProperty
(String property) getReference
(String genomeVersion) Get a property as a stringGet a property as a stringboolean
isDebug()
boolean
boolean
boolean
boolean
isHgvs()
boolean
boolean
boolean
boolean
boolean
boolean
isQuiet()
boolean
boolean
iterator()
keys()
Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)String[]
propertyToStringArray
(String attr) Parse a comma separated property as a string arraystatic Config
reset()
void
setDebug
(boolean debug) void
setErrorChromoHit
(boolean errorChromoHit) void
setErrorOnMissingChromo
(boolean errorOnMissingChromo) void
setExpandIub
(boolean expandIub) void
setHgvsOld
(boolean hgvsDnaOld) void
setHgvsOneLetterAA
(boolean hgvsOneLetterAa) void
setHgvsShift
(boolean hgvsShift) void
setHgvsTrId
(boolean hgvsTrId) void
setOnlyRegulation
(boolean onlyRegulation) void
setQuiet
(boolean quiet) void
setSnpEffectPredictor
(SnpEffectPredictor snpEffectPredictor) void
void
setTreatAllAsProteinCoding
(boolean treatAllAsProteinCoding) void
setUseHgvs
(boolean useHgvs) void
setVerbose
(boolean verbose) toString()
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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DEFAULT_CONFIG_FILE
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ETC_CONFIG_FILE
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PREFERRED_CONFIG_FILE
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DEFAULT_DATA_DIR
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KEY_BUNDLE_SUFIX
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KEY_CODON_PREFIX
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KEY_CODONTABLE_SUFIX
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KEY_COORDINATES
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KEY_DATA_DIR
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KEY_DATABASE_LOCAL
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KEY_DATABASE_REPOSITORY
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KEY_DATABASE_REPOSITORY_KEY
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KEY_DBNSFP_FIELDS
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KEY_GENOME_SUFIX
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KEY_LOF_IGNORE_PROTEIN_CODING_AFTER
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KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE
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KEY_LOF_DELETE_PROTEIN_CODING_BASES
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KEY_REFERENCE_SUFIX
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KEY_VERSIONS_URL
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COMPATIBLE_WITH_5_2
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COMPATIBLE_WITH_5_1
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DATABASE_COMPATIBLE_VERSIONS
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GENOMES_DIR
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DEFAULT_COORDINATES
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Constructor Details
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Config
This constructor is used in test cases -
Config
Create a config (uses DEFAULT_CONFIG_FILE) -
Config
Create a configuration from 'configFileName' -
Config
public Config(String genomeVersion, String configFileName, String dataDir, Map<String, String> override) Create a configuration from 'configFileName' -
Config
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Method Details
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get
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reset
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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
Get a list of URLs that can be used to download a database Use compatible versions from 'getDatabaseCompatibilityVersions()' -
downloadUrl
Build the URL for downloading a database fileFormat : 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
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getBaseFileNameGenes
Genes file path (no extension) -
getBaseFileNameMotif
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getBaseFileNameRegulation
Regulation file (GFF format) -
getBaseFileNameSequence
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getBundleName
Is this genome packed in a bundle? -
getConfigFileName
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getConfigFileCanonicaPath
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getCoordinates
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getDatabaseCompatibilityVersions
Return a list of databases that are compatible with this SnpEff version number -
getDatabaseLocal
Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc. -
getDatabaseLocalKey
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getDatabaseRepository
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getDatabaseRepository
Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc. -
getDatabaseRepositoryUrl
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getDbNsfpFields
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getDirData
Main data directory -
getDirDataGenomeVersion
Data dir for a specific genome version (i.e. where the database is) -
getDirMain
Main dir -
getDirRegulationBed
Directory where regulation 'BED' files are -
getDouble
Get a property as a double -
getFileListGenomeFasta
Filenames for reference sequence (fasta files) -
getFileNameCds
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getFileNameGenomeFasta
Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that exists -
getFileNameProteins
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getFileNameSequence
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getFileNameSequence
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getFileSnpEffectPredictor
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getGenome
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getGenome
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getGenomeVersion
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getLofDeleteProteinCodingBases
public double getLofDeleteProteinCodingBases() -
getLofIgnoreProteinCodingAfter
public double getLofIgnoreProteinCodingAfter() -
getLofIgnoreProteinCodingBefore
public double getLofIgnoreProteinCodingBefore() -
getLong
Get a property as a long -
getName
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getProperty
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propertyToStringArray
Parse a comma separated property as a string array -
getReference
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getSnpEffectPredictor
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setSnpEffectPredictor
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getString
Get a property as a string -
getString
Get a property as a string -
getVersionsUrl
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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
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keys
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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
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setUseHgvs
public void setUseHgvs(boolean useHgvs) -
toString
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