Package org.snpsift.fileIterator

Class DbNsfp

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

  • Field Details

    • DATA_TYPES_CACHE_EXT

      public static final String DATA_TYPES_CACHE_EXT
      See Also:

    • DATA_TYPES_MIN_LINES

      public static final int DATA_TYPES_MIN_LINES
      See Also:

    • DATA_TYPES_MAX_LINES

      public static final int DATA_TYPES_MAX_LINES
      See Also:

    • HEADER_PREFIX

      public static final String HEADER_PREFIX
      See Also:

    • COLUMN_SEPARATOR

      public static final String COLUMN_SEPARATOR
      See Also:

    • SUBFIELD_SEPARATOR_CHAR

      public static final char SUBFIELD_SEPARATOR_CHAR
      See Also:

    • SUBFIELD_SEPARATOR

      public static final String SUBFIELD_SEPARATOR
      See Also:

    • SUBFIELD_SEPARATOR_CHAR_2

      public static final char SUBFIELD_SEPARATOR_CHAR_2
      See Also:

    • SUBFIELD_SEPARATOR_2

      public static final String SUBFIELD_SEPARATOR_2
      See Also:

    • COLUMN_CHR_NAME

      public static final String COLUMN_CHR_NAME
      See Also:

    • COLUMN_POS_NAME_v2

      public static final String COLUMN_POS_NAME_v2
      See Also:

    • COLUMN_POS_NAME_v3

      public static final String COLUMN_POS_NAME_v3
      See Also:

    • ALT_NAME

      public static final String ALT_NAME
      See Also:

    • REF_NAME

      public static final String REF_NAME
      See Also:

    • fileName

      protected 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 String[] fieldNames

    • types

      protected org.snpeff.vcf.VcfInfoType[] types

    • genome

      protected org.snpeff.interval.Genome genome

    • names2index

      protected HashMap<String,Integer> names2index

    • tabixReader

      protected htsjdk.tribble.readers.TabixReader tabixReader

    • latestResults

      protected List<DbNsfpEntry> latestResults

    • latestResultsInterval

      protected org.snpeff.interval.Marker latestResultsInterval

  • Constructor Details

    • DbNsfp

      public DbNsfp(String fileName)

  • Method Details

    • 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(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 String getFieldName(int idx)

    • getFieldNames

      public Set<String> getFieldNames()

    • getFieldNamesSorted

      public String[] getFieldNamesSorted()

    • getIndex

      public int getIndex(String name)

    • getNames2index

      public HashMap<String,Integer> getNames2index()

    • getRefIdx

      public int getRefIdx()

    • getStartIdx

      public int getStartIdx()

    • getTypes

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

    • guessDataType

      protected org.snpeff.vcf.VcfInfoType guessDataType(String value)
      Guess value type

    • guessDataTypes

      protected boolean guessDataTypes()
      Guess data types from file

    • hasField

      public boolean hasField(String filedName)
      Do we have a column 'colName'?

    • initTabix

      protected boolean initTabix(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 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(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>