public class DbSnpBitSetUtil extends Object
Modifier and Type | Class and Description |
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static class |
DbSnpBitSetUtil.DbSnpBitSets
Little tuple class to contain one bitset for SNPs and another for Indels.
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Constructor and Description |
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DbSnpBitSetUtil(File dbSnpFile,
SAMSequenceDictionary sequenceDictionary)
Constructor that creates a bit set with bits set to true for all variant types.
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DbSnpBitSetUtil(File dbSnpFile,
SAMSequenceDictionary sequenceDictionary,
Collection<VariantType> variantsToMatch)
Constructor.
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Modifier and Type | Method and Description |
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static DbSnpBitSetUtil.DbSnpBitSets |
createSnpAndIndelBitSets(File dbSnpFile,
SAMSequenceDictionary sequenceDictionary)
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
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boolean |
isDbSnpSite(String sequenceName,
int pos)
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
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public DbSnpBitSetUtil(File dbSnpFile, SAMSequenceDictionary sequenceDictionary)
public DbSnpBitSetUtil(File dbSnpFile, SAMSequenceDictionary sequenceDictionary, Collection<VariantType> variantsToMatch)
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.public static DbSnpBitSetUtil.DbSnpBitSets createSnpAndIndelBitSets(File dbSnpFile, SAMSequenceDictionary sequenceDictionary)
public boolean isDbSnpSite(String sequenceName, int pos)