Package org.broadinstitute.hellbender.engine
package org.broadinstitute.hellbender.engine
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ClassDescriptionBase class for concordance walkers, which process one variant at a time from one or more sources of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.store a truth vc in case of a false negative, an eval vc in case of a false positive, or a concordance pair of truth and eval in case of a true positive.Given a
MultiIntervalShardofGATKRead, iterates over each locus within that shard, and calculates theActivityProfileStatethere, using the providedAssemblyRegionEvaluatorto determine if each site is active.Bundles together and AlignmentContext and a ReferenceContextBundles together a pileup and a location.Region of the genome that gets assembled by the local assembly engine.Classes that implement this interface have the ability to evaluate how likely it is that a site is "active" (contains potential real variation).Given an iterator ofActivityProfileState, findsAssemblyRegions.Given aMultiIntervalShardofGATKRead, iterates over eachAssemblyRegionwithin that shard, using the providedAssemblyRegionEvaluatorto determine the boundaries between assembly regions.An AssemblyRegionWalker is a tool that processes an entire region of reads at a time, each marked as either "active" (containing possible variation) or "inactive" (not likely to contain actual variation).A source of reference base calls.Classes annotated with this annotation are NOT intended or designed to be extended and should be treated as final.A walker that processes duplicate reads that share the same Unique molecule Identifier (UMI) as a single unit.Wrapper around FeatureManager that presents Feature data from a particular interval to a client tool without improperly exposing engine internals.FeatureDataSource<T extends htsjdk.tribble.Feature>Enables traversals and queries over sources of Features, which are metadata associated with a location on the genome in a format supported by our file parsing framework, Tribble.FeatureInput<T extends htsjdk.tribble.Feature>Class to represent a Feature-containing input file.Handles discovery of available codecs and Feature arguments, file format detection and codec selection, and creation/management/querying of FeatureDataSources for each source of Features.FeatureWalker<F extends htsjdk.tribble.Feature>A FeatureWalker is a tool that processes aFeatureat a time from a source of Features, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.A GATKDataSource is something that can be iterated over from start to finish and/or queried by genomic interval.GATK tool command line arguments that are input or output resources.Base class for all GATK tools.An IntervalWalker is a tool that processes a single interval at a time, with the ability to query optional overlapping sources of reads, reference data, and/or variants/features.A LocusWalker is a tool that processes reads that overlap a single position in a reference at a time from one or multiple sources of reads, with optional contextual information from a reference and/or sets of variants/Features.An implementation ofLocusWalkerthat supports arbitrary interval side inputs.MultiFeatureWalker<F extends htsjdk.tribble.Feature>A MultiFeatureWalker is a tool that presents oneFeatureat a time in sorted order from multiple sources of Features.MultiFeatureWalker.MergingIterator<F extends htsjdk.tribble.Feature>MultiFeatureWalker.PQContext<F extends htsjdk.tribble.Feature>MultiFeatureWalker.PQEntry<F extends htsjdk.tribble.Feature>A class to represent shards of read data spanning multiple intervals.An interface to represent shards of arbitrary data spanning multiple intervals.A MultiplePassReadWalker traverses input reads multiple times.Implemented by MultiplePassReadWalker-derived tools.A VariantWalker that makes multiple passes through the variants.MultiVariantDataSource aggregates multiple FeatureDataSources of variants, and enables traversals and queries over those sources through a single interface.A MultiVariantWalker is a tool that processes one variant at a time, in position order, from multiple sources of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.A MultiVariantWalker that walks over multiple variant context sources in reference order and emits to client tools groups of all input variant contexts by their start position.A specialized read walker that may be gracefully stopped before the input stream ends A tool derived from this class should implementPartialReadWalker.shouldExitEarly(GATKRead)to indicate when to stop.A basic progress meter to print out the number of records processed (and other metrics) during a traversal at a configurable time interval.ReadContextData is additional data that's useful when processing reads.A cut-down version ofAssemblyRegionthat doesn't store reads, used in the strict implementation ofFindAssemblyRegionsSpark.Wrapper around ReadsDataSource that presents reads overlapping a specific interval to a client, without improperly exposing the entire ReadsDataSource interface.An interface for managing traversals over sources of reads.Manages traversals and queries over sources of reads which are accessible viaPaths (for now, SAM/BAM/CRAM files only).A ReadWalker is a tool that processes a single read at a time from one or multiple sources of reads, with optional contextual information from a reference and/or sets of variants/Features.Wrapper around ReferenceDataSource that presents data from a specific interval/window to a client, without improperly exposing the entire ReferenceDataSource interface.Manages traversals and queries over reference data.Manages traversals and queries over reference data (for now, fasta files only) Supports targeted queries over the reference by interval, but does not yet support complete iteration over the entire reference.Manages traversals and queries over in-memory reference data.ReferenceShard is section of the reference genome that's used for sharding work for pairing things with the reference.A reference walker is a tool which processes each base in a given reference.Shard<T>A Shard of records of type T covering a specific genomic interval, optionally expanded by a configurable amount of padded data, that provides the ability to iterate over its records.Holds the bounds of aShard, both with and without paddingAShardbacked by aShardBoundaryand a collection of records.adapts a normal Shard into a MultiIntervalShard that contains only the single wrapped shard this is a temporary shim until we can fully adopt MultiIntervalShard in HaplotypeCallerSparkA simple container class for parameters controlling which records get returned during traversals.VariantLocusWalker processes variants from a single source, grouped by locus overlap, or optionally one at a time in order, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.VariantShard is section of the genome that's used for sharding work for pairing things with variants.A VariantWalker is a tool that processes a variant at a time from a source of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.Base class for variant walkers, which process variants from one or more sources of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features.Base class for pre-packaged walker traversals in the GATK engine.