Package org.snpsift.annotate.mem.database

Class VariantDatabase

java.lang.Object
org.snpsift.annotate.mem.database.VariantDatabase
public class VariantDatabase extends Object
A database of variant's data used to annotate a VCF file (i.e. VCF entries). The database only loads one chromosome at a time, to speed up the process while fitting in memory. The database is a collection of VariantDatabaseChr objects, one per chromosome. Each 'VariantDatabaseChr' is stored in one file per chromosome. 'VariantDatabase' manages the 'VariantDatabaseChr' files (loading, saving, etc).

  • Field Details

  • Constructor Details

    • VariantDatabase

      public VariantDatabase()

    • VariantDatabase

      public VariantDatabase(String databaseVcfFileName, String dbDir, String[] fieldNamesCreate)
      Constructor used to create a database

    • VariantDatabase

      public VariantDatabase(String databaseVcfFileName, String dbDir, String[] fieldNamesAnnotate, String prefix, boolean emptyIfNotFound)
      Constructor used to annotate a database

  • Method Details

    • dbDirFromVcfFileName

      public static String dbDirFromVcfFileName(String dbFileName)
      Get the database directory name from a "VCF database" file name buy just appending ".snpsift.vardb"

    • add

      protected void add(org.snpeff.vcf.VariantVcfEntry variantVcfEntry)
      Add a VCF entry to the database

    • annotate

      public int annotate(org.snpeff.vcf.VcfEntry vcfEntry)
      This method is used to annotate a VCF entry The annotations are added to the INFO field of the VCF entry

    • checkFields

      public boolean checkFields(String[] fieldNames, boolean throwExceptionOnError)
      Check that all `fieldNames` are available in `fields`
      Returns:
      true is all fieldsNames are present, false otherwise

    • create

      public void create(String vcfContents)
      Create a database from a VCF file content (as a string) This is used for testing

    • create

      public void create()
      Create a database from a VCF file

    • get

      public VariantDataFrame get(String chr)
      Get the database for a chromosome

    • getDatabaseVcfFileName

      public String getDatabaseVcfFileName()

    • getDbDir

      public String getDbDir()

    • getFields

      public Fields getFields()

    • getVariantTypeCounters

      public VariantTypeCounters getVariantTypeCounters()

    • load

      public void load()

    • parseVcfHeaderFields

      protected Fields parseVcfHeaderFields(String databaseVcfFileName)
      Read VCF header and get columns data types
      Parameters:
      databaseVcfFileName -

    • parseVcfHeaderFields

      protected Fields parseVcfHeaderFields(org.snpeff.fileIterator.VcfFileIterator vcfFileIterator)
      Read VCF header and get columns data types
      Parameters:
      databaseVcfFileName -

    • save

      public void save()

    • setDbDir

      public void setDbDir(String dbDir)

    • setFieldNamesAnnotate

      public void setFieldNamesAnnotate(String[] fieldNamesAnnotate)

    • setPrefix

      public void setPrefix(String prefix)

    • setVerbose

      public void setVerbose(boolean verbose)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • vcfHeaders

      public Collection<org.snpeff.vcf.VcfHeaderEntry> vcfHeaders()