Package picard.util

Class DbSnpBitSetUtil

java.lang.Object
picard.util.DbSnpBitSetUtil

public class DbSnpBitSetUtil extends Object
Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static class 
    Little tuple class to contain one bitset for SNPs and another for Indels.
  • Constructor Summary

    Constructors
    Constructor
    Description
    DbSnpBitSetUtil(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
    Constructor that creates a bit set with bits set to true for all variant types.
    DbSnpBitSetUtil(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch)
    Constructor that creates a bit set with bits set to true for the given variant types.
    DbSnpBitSetUtil(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch, htsjdk.samtools.util.IntervalList intervals)
    Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
    DbSnpBitSetUtil(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch, htsjdk.samtools.util.IntervalList intervals, Optional<htsjdk.samtools.util.Log> log)
    Constructor.
    DbSnpBitSetUtil(Path dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
    Constructor that creates a bit set with bits set to true for all variant types.
    DbSnpBitSetUtil(Path dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch)
    Constructor that creates a bit set with bits set to true for the given variant types.
    DbSnpBitSetUtil(Path dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch, htsjdk.samtools.util.IntervalList intervals)
    Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
    DbSnpBitSetUtil(Path dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch, htsjdk.samtools.util.IntervalList intervals, Optional<htsjdk.samtools.util.Log> log)
    Constructor.
  • Method Summary

    Modifier and Type
    Method
    Description
    createSnpAndIndelBitSets(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
    Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
    createSnpAndIndelBitSets(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, htsjdk.samtools.util.IntervalList intervals)
    Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
    createSnpAndIndelBitSets(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, htsjdk.samtools.util.IntervalList intervals, Optional<htsjdk.samtools.util.Log> log)
    Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
    createSnpAndIndelBitSets(PicardHtsPath dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, htsjdk.samtools.util.IntervalList intervals)
    Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
    createSnpAndIndelBitSets(PicardHtsPath dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, htsjdk.samtools.util.IntervalList intervals, Optional<htsjdk.samtools.util.Log> log)
    Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
    boolean
    isDbSnpSite(String sequenceName, int pos)
    Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • DbSnpBitSetUtil

      public DbSnpBitSetUtil(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
      Constructor that creates a bit set with bits set to true for all variant types.
    • DbSnpBitSetUtil

      public DbSnpBitSetUtil(Path dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
      Constructor that creates a bit set with bits set to true for all variant types.
    • DbSnpBitSetUtil

      public DbSnpBitSetUtil(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch)
      Constructor that creates a bit set with bits set to true for the given variant types.
    • DbSnpBitSetUtil

      public DbSnpBitSetUtil(Path dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch)
      Constructor that creates a bit set with bits set to true for the given variant types.
    • DbSnpBitSetUtil

      public DbSnpBitSetUtil(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch, htsjdk.samtools.util.IntervalList intervals)
      Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
    • DbSnpBitSetUtil

      public DbSnpBitSetUtil(Path dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch, htsjdk.samtools.util.IntervalList intervals)
      Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
    • DbSnpBitSetUtil

      public DbSnpBitSetUtil(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch, htsjdk.samtools.util.IntervalList intervals, Optional<htsjdk.samtools.util.Log> log)
      Constructor. For each sequence, creates a BitSet that denotes whether a dbSNP entry is present at each base in the reference sequence. The set is reference.length() + 1 so that it can be indexed by 1-based reference base. True means dbSNP present, false means no dbSNP present.
      Parameters:
      dbSnpFile - in VCF format.
      sequenceDictionary - Optionally, a sequence dictionary corresponding to the dbSnp file, else null. If present, BitSets will be allocated more efficiently because the maximum size will be known.
      variantsToMatch - what types of variants to load.
      intervals - an interval list specifying the regions to load, or null, if we are return all dbSNP sites.
    • DbSnpBitSetUtil

      public DbSnpBitSetUtil(Path dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch, htsjdk.samtools.util.IntervalList intervals, Optional<htsjdk.samtools.util.Log> log)
      Constructor. For each sequence, creates a BitSet that denotes whether a dbSNP entry is present at each base in the reference sequence. The set is reference.length() + 1 so that it can be indexed by 1-based reference base. True means dbSNP present, false means no dbSNP present.
      Parameters:
      dbSnpFile - in VCF format.
      sequenceDictionary - Optionally, a sequence dictionary corresponding to the dbSnp file, else null. If present, BitSets will be allocated more efficiently because the maximum size will be known.
      variantsToMatch - what types of variants to load.
      intervals - an interval list specifying the regions to load, or null, if we are return all dbSNP sites.
  • Method Details

    • createSnpAndIndelBitSets

      public static DbSnpBitSetUtil.DbSnpBitSets createSnpAndIndelBitSets(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
      Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
    • createSnpAndIndelBitSets

      public static DbSnpBitSetUtil.DbSnpBitSets createSnpAndIndelBitSets(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, htsjdk.samtools.util.IntervalList intervals)
      Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF. If intervals are given, consider only SNP and indel sites that overlap the intervals.
    • createSnpAndIndelBitSets

      public static DbSnpBitSetUtil.DbSnpBitSets createSnpAndIndelBitSets(PicardHtsPath dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, htsjdk.samtools.util.IntervalList intervals)
      Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF. If intervals are given, consider only SNP and indel sites that overlap the intervals.
    • createSnpAndIndelBitSets

      public static DbSnpBitSetUtil.DbSnpBitSets createSnpAndIndelBitSets(File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, htsjdk.samtools.util.IntervalList intervals, Optional<htsjdk.samtools.util.Log> log)
      Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF. If intervals are given, consider only SNP and indel sites that overlap the intervals. If log is given, progress loading the variants will be written to the log.
    • createSnpAndIndelBitSets

      public static DbSnpBitSetUtil.DbSnpBitSets createSnpAndIndelBitSets(PicardHtsPath dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, htsjdk.samtools.util.IntervalList intervals, Optional<htsjdk.samtools.util.Log> log)
      Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF. If intervals are given, consider only SNP and indel sites that overlap the intervals. If log is given, progress loading the variants will be written to the log.
    • isDbSnpSite

      public boolean isDbSnpSite(String sequenceName, int pos)
      Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false