Package org.snpsift.fileIterator

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>