org.broadinstitute.hellbender.engine

Class MultiVariantDataSource

java.lang.Object

org.broadinstitute.hellbender.engine.MultiVariantDataSource

All Implemented Interfaces:

java.lang.AutoCloseable, java.lang.Iterable<htsjdk.variant.variantcontext.VariantContext>, GATKDataSource<htsjdk.variant.variantcontext.VariantContext>

public final class MultiVariantDataSource
extends java.lang.Object
implements GATKDataSource<htsjdk.variant.variantcontext.VariantContext>, java.lang.AutoCloseable

MultiVariantDataSource aggregates multiple FeatureDataSources of variants, and enables traversals and queries over those sources through a single interface. Two basic operations are available on this data source: -Iteration over all Variants in the data sources, optionally restricted to Variants overlapping a set of intervals if intervals are provided via setIntervalsForTraversal(List). Traversal by a set of intervals requires the files to have been indexed using the bundled tool IndexFeatureFile. The set of intervals provided MUST be non-overlapping and sorted in increasing order of start position. -Targeted queries by one interval at a time. This also requires the files to have been indexed using the bundled tool IndexFeatureFile. Targeted queries by one interval at a time are unaffected by any intervals for full traversal set via setIntervalsForTraversal(List).

Constructor Summary

Constructors

Constructor and Description
MultiVariantDataSource(java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> featureInputs, int queryLookaheadBases) Creates a MultiVariantDataSource backed by the provided FeatureInputs.
MultiVariantDataSource(java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> featureInputs, int queryLookaheadBases, int cloudPrefetchBuffer, int cloudIndexPrefetchBuffer, java.nio.file.Path reference, boolean skipDictionaryValidation) Creates a MultiVariantDataSource backed by the provided FeatureInputs.

Method Summary

Modifier and Type	Method and Description
void	close() Permanently close this data source, invalidating any open iteration over it, and making it invalid for future iterations and queries.
htsjdk.variant.vcf.VCFHeader	getHeader() Gets the merged header associated with this data source
java.lang.String	getName() Get the logical name of this data source.
java.util.SortedSet<java.lang.String>	getSamples() Return lexicographically sorted set of uniquified sample names merged from across input data sources
htsjdk.samtools.SAMSequenceDictionary	getSequenceDictionary() Returns the aggregate sequence dictionary for this source of Variants.
java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>	iterator() Gets an iterator over all variants in this data source, restricting traversal to variants overlapping our intervals if intervals were provided via setIntervalsForTraversal(List) Calling this method invalidates (closes) any previous iterator obtained from this method.
java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>	query(SimpleInterval interval) Gets an iterator over all Variants in this data source that overlap the provided interval.
void	setIntervalsForTraversal(java.util.List<SimpleInterval> intervals) Restricts traversals of this data source via iterator() to only return variants that overlap the provided intervals.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

MultiVariantDataSource

public MultiVariantDataSource(java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> featureInputs,
                              int queryLookaheadBases)

Creates a MultiVariantDataSource backed by the provided FeatureInputs. We will look ahead the specified number of bases during queries that produce cache misses.

Parameters:

featureInputs - List of FeatureInput> specifying sources of VariantContexts

queryLookaheadBases - look ahead this many bases during queries that produce cache misses

MultiVariantDataSource

public MultiVariantDataSource(java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> featureInputs,
                              int queryLookaheadBases,
                              int cloudPrefetchBuffer,
                              int cloudIndexPrefetchBuffer,
                              java.nio.file.Path reference,
                              boolean skipDictionaryValidation)

Creates a MultiVariantDataSource backed by the provided FeatureInputs. We will look ahead the specified number of bases during queries that produce cache misses.

Parameters:

featureInputs - List of FeatureInput> specifying sources of VariantContexts

queryLookaheadBases - look ahead this many bases during queries that produce cache misses

cloudPrefetchBuffer - MB size of caching/prefetching wrapper for the data, if on Google Cloud (0 to disable).

cloudIndexPrefetchBuffer - MB size of caching/prefetching wrapper for the index, if on Google Cloud (0 to disable).

reference - reference to use when creating FeatureDataSources, may be null, only needed by GenomicsDB

Method Detail

getSequenceDictionary

public htsjdk.samtools.SAMSequenceDictionary getSequenceDictionary()

Returns the aggregate sequence dictionary for this source of Variants. Uses the dictionary resulting from merging available individual VCF headers (if present) for variant inputs.

Returns:

the sequence dictionary derived from the input sources, or null if no dictionary could be created from any header or index file.

getHeader

public htsjdk.variant.vcf.VCFHeader getHeader()

Gets the merged header associated with this data source

Returns:

header associated with this data source as an Object

setIntervalsForTraversal

public void setIntervalsForTraversal(java.util.List<SimpleInterval> intervals)

Restricts traversals of this data source via iterator() to only return variants that overlap the provided intervals. Calls to query(SimpleInterval) are not affected by these intervals. Intervals MUST be non-overlapping and sorted in order of increasing start position, otherwise traversal results will be incorrect. Passing in a null or empty interval List clears the intervals for traversal, making future iterations over this data source unrestricted by intervals.

Parameters:

intervals - Our next full traversal will return only variants overlapping these intervals

iterator

public java.util.Iterator<htsjdk.variant.variantcontext.VariantContext> iterator()

Gets an iterator over all variants in this data source, restricting traversal to variants overlapping our intervals if intervals were provided via setIntervalsForTraversal(List) Calling this method invalidates (closes) any previous iterator obtained from this method.

Specified by:

iterator in interface java.lang.Iterable<htsjdk.variant.variantcontext.VariantContext>

Returns:

an iterator over all variants in this data source, limited to variants that overlap the intervals supplied via setIntervalsForTraversal(List) (if intervals were provided)

query

public java.util.Iterator<htsjdk.variant.variantcontext.VariantContext> query(SimpleInterval interval)

Gets an iterator over all Variants in this data source that overlap the provided interval. This operation is not affected by intervals provided via setIntervalsForTraversal(List). Requires the backing files to have been indexed using the IndexFeatureFile tool, and to be sorted in increasing order of start position for each contig. Query results are cached to improve the performance of future queries during typical access patterns. See notes to the class as a whole for a description of the caching strategy. Calling this method potentially invalidates (closes) any other open iterator obtained from this data source via a call to iterator()

Specified by:

query in interface GATKDataSource<htsjdk.variant.variantcontext.VariantContext>

Parameters:

interval - retrieve all Variants overlapping this interval

Returns:

an iterator over all Variants in this data source that overlap the provided interval

getName

public java.lang.String getName()

Get the logical name of this data source.

Returns:

the logical name of this data source

close

public void close()

Permanently close this data source, invalidating any open iteration over it, and making it invalid for future iterations and queries.

Specified by:

close in interface java.lang.AutoCloseable

getSamples

public java.util.SortedSet<java.lang.String> getSamples()

Return lexicographically sorted set of uniquified sample names merged from across input data sources