Class DbNsfp

  • All Implemented Interfaces:
    DbMarker<org.snpeff.interval.Variant,​DbNsfpEntry>

    public class DbNsfp
    extends java.lang.Object
    implements DbMarker<org.snpeff.interval.Variant,​DbNsfpEntry>
    DbNSFP database: Reference https://sites.google.com/site/jpopgen/dbNSFP
    Author:
    pcingola, lletourn (original author)
    • Field Detail

      • DATA_TYPES_CACHE_EXT

        public static final java.lang.String DATA_TYPES_CACHE_EXT
        See Also:
        Constant Field Values
      • COLUMN_SEPARATOR

        public static final java.lang.String COLUMN_SEPARATOR
        See Also:
        Constant Field Values
      • SUBFIELD_SEPARATOR_CHAR

        public static final char SUBFIELD_SEPARATOR_CHAR
        See Also:
        Constant Field Values
      • SUBFIELD_SEPARATOR

        public static final java.lang.String SUBFIELD_SEPARATOR
        See Also:
        Constant Field Values
      • SUBFIELD_SEPARATOR_CHAR_2

        public static final char SUBFIELD_SEPARATOR_CHAR_2
        See Also:
        Constant Field Values
      • SUBFIELD_SEPARATOR_2

        public static final java.lang.String SUBFIELD_SEPARATOR_2
        See Also:
        Constant Field Values
      • COLUMN_POS_NAME_v2

        public static final java.lang.String COLUMN_POS_NAME_v2
        See Also:
        Constant Field Values
      • COLUMN_POS_NAME_v3

        public static final java.lang.String COLUMN_POS_NAME_v3
        See Also:
        Constant Field Values
      • fileName

        protected java.lang.String fileName
      • debug

        protected boolean debug
      • multipleValues

        protected boolean[] multipleValues
      • verbose

        protected boolean verbose
      • chromosomeIdx

        protected int chromosomeIdx
      • startIdx

        protected int startIdx
      • altIdx

        protected int altIdx
      • refIdx

        protected int refIdx
      • maxChrPosRefAltIdx

        protected int maxChrPosRefAltIdx
      • fieldNames

        protected java.lang.String[] fieldNames
      • types

        protected org.snpeff.vcf.VcfInfoType[] types
      • genome

        protected org.snpeff.interval.Genome genome
      • names2index

        protected java.util.HashMap<java.lang.String,​java.lang.Integer> names2index
      • tabixReader

        protected htsjdk.tribble.readers.TabixReader tabixReader
      • latestResults

        protected java.util.List<DbNsfpEntry> latestResults
      • latestResultsInterval

        protected org.snpeff.interval.Marker latestResultsInterval
    • Constructor Detail

      • DbNsfp

        public DbNsfp​(java.lang.String fileName)
    • Method Detail

      • close

        public void close()
        Description copied from interface: DbMarker
        Close database, free resources
        Specified by:
        close in interface DbMarker<org.snpeff.interval.Variant,​DbNsfpEntry>
      • dataTypes

        protected boolean dataTypes()
        Guess field types: Read many lines and guess the data type for each column
      • forceMissingTypesAsString

        public void forceMissingTypesAsString()
        Force missing types as string
      • getAltIdx

        public int getAltIdx()
      • getChrPosRefAltIdx

        public int getChrPosRefAltIdx()
      • getChromosome

        public org.snpeff.interval.Chromosome getChromosome​(java.lang.String chromoName)
        Find chromosome 'chromoName'. If it does not exists and 'createChromos' is true, the chromosome is created
      • getChromosomeIdx

        public int getChromosomeIdx()
      • getFieldCount

        public int getFieldCount()
      • getFieldName

        public java.lang.String getFieldName​(int idx)
      • getFieldNames

        public java.util.Set<java.lang.String> getFieldNames()
      • getFieldNamesSorted

        public java.lang.String[] getFieldNamesSorted()
      • getIndex

        public int getIndex​(java.lang.String name)
      • getNames2index

        public java.util.HashMap<java.lang.String,​java.lang.Integer> getNames2index()
      • getRefIdx

        public int getRefIdx()
      • getStartIdx

        public int getStartIdx()
      • getTypes

        public org.snpeff.vcf.VcfInfoType[] getTypes()
      • guessDataType

        protected org.snpeff.vcf.VcfInfoType guessDataType​(java.lang.String value)
        Guess value type
      • guessDataTypes

        protected boolean guessDataTypes()
        Guess data types from file
      • hasField

        public boolean hasField​(java.lang.String filedName)
        Do we have a column 'colName'?
      • initTabix

        protected boolean initTabix​(java.lang.String fileName)
        Initialize tabix reader
      • match

        protected boolean match​(org.snpeff.interval.Variant var,
                                DbNsfpEntry dbEntry)
        Does database entry 'DbNsfpEntry' match 'variant'?
      • open

        public void open()
        Description copied from interface: DbMarker
        Open database (load index in memory if required)
        Specified by:
        open in interface DbMarker<org.snpeff.interval.Variant,​DbNsfpEntry>
      • query

        public java.util.Collection<DbNsfpEntry> query​(org.snpeff.interval.Variant variant)
        Query tabix file to get dbNsfp entries (or cached entries from latest results)
        Specified by:
        query in interface DbMarker<org.snpeff.interval.Variant,​DbNsfpEntry>
        Parameters:
        variant - : Variant to query in DnNSFP
        Returns:
        A list of result
      • saveDataTypesCache

        protected void saveDataTypesCache​(java.lang.String cacheFileName)
        Save data types to cache file
      • setDebug

        public void setDebug​(boolean debug)
        Specified by:
        setDebug in interface DbMarker<org.snpeff.interval.Variant,​DbNsfpEntry>
      • setVerbose

        public void setVerbose​(boolean verbose)
        Specified by:
        setVerbose in interface DbMarker<org.snpeff.interval.Variant,​DbNsfpEntry>