picard.util

Class DbSnpBitSetUtil

java.lang.Object

picard.util.DbSnpBitSetUtil

public class DbSnpBitSetUtil
extends java.lang.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 and Description
static class	DbSnpBitSetUtil.DbSnpBitSets Little tuple class to contain one bitset for SNPs and another for Indels.

Constructor Summary

Constructors

Constructor and Description
DbSnpBitSetUtil(java.io.File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary) Constructor that creates a bit set with bits set to true for all variant types.
DbSnpBitSetUtil(java.io.File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, java.util.Collection<VariantType> variantsToMatch) Constructor.

Method Summary

Modifier and Type	Method and Description
static DbSnpBitSetUtil.DbSnpBitSets	createSnpAndIndelBitSets(java.io.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.
boolean	isDbSnpSite(java.lang.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 Detail

DbSnpBitSetUtil

public DbSnpBitSetUtil(java.io.File dbSnpFile,
                       htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)

Constructor that creates a bit set with bits set to true for all variant types.

DbSnpBitSetUtil

public DbSnpBitSetUtil(java.io.File dbSnpFile,
                       htsjdk.samtools.SAMSequenceDictionary sequenceDictionary,
                       java.util.Collection<VariantType> variantsToMatch)

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.

Method Detail

createSnpAndIndelBitSets

public static DbSnpBitSetUtil.DbSnpBitSets createSnpAndIndelBitSets(java.io.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.

isDbSnpSite

public boolean isDbSnpSite(java.lang.String sequenceName,
                           int pos)

Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false