| Interface | Description |
|---|---|
| AssemblyRegionEvaluator |
Classes that implement this interface have the ability to evaluate how likely it is that a site is "active"
(contains potential real variation).
|
| BasicReference |
A source of reference base calls.
|
| GATKDataSource<T> |
A GATKDataSource is something that can be iterated over from start to finish
and/or queried by genomic interval.
|
| MultiIntervalShard<T> |
An interface to represent shards of arbitrary data spanning multiple intervals.
|
| MultiplePassReadWalker.GATKReadConsumer |
Implemented by MultiplePassReadWalker-derived tools.
|
| ReadsDataSource |
An interface for managing traversals over sources of reads.
|
| ReferenceDataSource |
Manages traversals and queries over reference data.
|
| 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.
|
| Class | Description |
|---|---|
| AbstractConcordanceWalker |
Base 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.
|
| AbstractConcordanceWalker.TruthVersusEval |
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.
|
| ActivityProfileStateIterator |
Given a
MultiIntervalShard of GATKRead, iterates over each locus within
that shard, and calculates the ActivityProfileState there, using the provided AssemblyRegionEvaluator
to determine if each site is active. |
| AlignmentContext |
Bundles together a pileup and a location.
|
| AssemblyRegion |
Region of the genome that gets assembled by the local assembly engine.
|
| AssemblyRegionFromActivityProfileStateIterator |
Given an iterator of
ActivityProfileState, finds AssemblyRegions. |
| AssemblyRegionIterator |
Given a
MultiIntervalShard of GATKRead, iterates over each AssemblyRegion within
that shard, using the provided AssemblyRegionEvaluator to determine the boundaries between assembly
regions. |
| AssemblyRegionWalker |
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).
|
| DuplicateSetWalker |
A walker that processes duplicate reads that share the same Unique molecule Identifier (UMI) as a single unit.
|
| FeatureContext |
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.
|
| FeatureManager |
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 a
Feature at a time from a source of Features, with
optional contextual information from a reference, sets of reads, and/or supplementary sources
of Features. |
| GATKPath |
GATK tool command line arguments that are input or output resources.
|
| GATKTool |
Base class for all GATK tools.
|
| IntervalWalker |
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.
|
| LocusWalker |
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.
|
| LocusWalkerByInterval |
An implementation of
LocusWalker that supports arbitrary interval side inputs. |
| MultiIntervalLocalReadShard |
A class to represent shards of read data spanning multiple intervals.
|
| MultiplePassReadWalker |
A MultiplePassReadWalker traverses input reads multiple times.
|
| MultiplePassVariantWalker |
A VariantWalker that makes multiple passes through the variants.
|
| MultiVariantDataSource |
MultiVariantDataSource aggregates multiple FeatureDataSources of variants, and enables traversals and queries
over those sources through a single interface.
|
| MultiVariantWalker |
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.
|
| MultiVariantWalkerGroupedOnStart |
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.
|
| ProgressMeter |
A basic progress meter to print out the number of records processed (and other metrics) during a traversal
at a configurable time interval.
|
| ReadContextData |
ReadContextData is additional data that's useful when processing reads.
|
| ReadlessAssemblyRegion |
A cut-down version of
AssemblyRegion that doesn't store reads, used in the strict implementation of
FindAssemblyRegionsSpark. |
| ReadsContext |
Wrapper around ReadsDataSource that presents reads overlapping a specific interval to a client,
without improperly exposing the entire ReadsDataSource interface.
|
| ReadsDataSourcePool |
Pool of
ReadsDataSource instances. |
| ReadsPathDataSource |
Manages traversals and queries over sources of reads which are accessible via
Paths
(for now, SAM/BAM/CRAM files only). |
| ReadWalker |
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.
|
| ReferenceContext |
Wrapper around ReferenceDataSource that presents data from a specific interval/window to a client,
without improperly exposing the entire ReferenceDataSource interface.
|
| ReferenceFileSource |
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.
|
| ReferenceMemorySource |
Manages traversals and queries over in-memory reference data.
|
| ReferenceShard |
ReferenceShard is section of the reference genome that's used for sharding work for pairing things with
the reference.
|
| ReferenceWalker |
A reference walker is a tool which processes each base in a given reference.
|
| ShardBoundary |
Holds the bounds of a
Shard, both with and without padding |
| ShardBoundaryShard<T> |
A
Shard backed by a ShardBoundary and a collection of records. |
| ShardToMultiIntervalShardAdapter<T> |
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 HaplotypeCallerSpark
|
| TraversalParameters |
A simple container class for parameters controlling which records get returned during traversals.
|
| TwoPassVariantWalker | |
| VariantLocusWalker |
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 |
VariantShard is section of the genome that's used for sharding work for pairing things with
variants.
|
| VariantWalker |
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.
|
| VariantWalkerBase |
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.
|
| WalkerBase |
Base class for pre-packaged walker traversals in the GATK engine.
|
| Enum | Description |
|---|---|
| AlignmentContext.ReadOrientation |
| Annotation Type | Description |
|---|---|
| DoNotSubclass |
Classes annotated with this annotation are NOT intended or designed to be extended and should be treated as final.
|