public class DbSnpBitSetUtil
extends java.lang.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(java.io.File dbSnpFile,
htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
Constructor that creates a bit set with bits set to true for all variant types.
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DbSnpBitSetUtil(java.io.File dbSnpFile,
htsjdk.samtools.SAMSequenceDictionary sequenceDictionary,
java.util.Collection<VariantType> variantsToMatch)
Constructor that creates a bit set with bits set to true for the given variant types.
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DbSnpBitSetUtil(java.io.File dbSnpFile,
htsjdk.samtools.SAMSequenceDictionary sequenceDictionary,
java.util.Collection<VariantType> variantsToMatch,
htsjdk.samtools.util.IntervalList intervals)
Constructor.
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Modifier and Type | Method and Description |
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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.
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static DbSnpBitSetUtil.DbSnpBitSets |
createSnpAndIndelBitSets(java.io.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.
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boolean |
isDbSnpSite(java.lang.String sequenceName,
int pos)
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
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public DbSnpBitSetUtil(java.io.File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
public DbSnpBitSetUtil(java.io.File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, java.util.Collection<VariantType> variantsToMatch)
public DbSnpBitSetUtil(java.io.File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, java.util.Collection<VariantType> variantsToMatch, htsjdk.samtools.util.IntervalList intervals)
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.public static DbSnpBitSetUtil.DbSnpBitSets createSnpAndIndelBitSets(java.io.File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
public static DbSnpBitSetUtil.DbSnpBitSets createSnpAndIndelBitSets(java.io.File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, htsjdk.samtools.util.IntervalList intervals)
public boolean isDbSnpSite(java.lang.String sequenceName, int pos)