| Interface | Description |
|---|---|
| HasGenomeLocation |
Indicates that this object has a genomic location and provides a systematic interface to get it.
|
| IntervalPileup | |
| IntervalPileup.Element | |
| IntervalPileup.Insert | |
| MathUtils.IntToDoubleArrayFunction | |
| SerializableFunction<T,R> |
Represents a
Function that is Serializable. |
| Class | Description |
|---|---|
| AutoCloseableReference<T> |
Reference to another object that perform some action when closed.
|
| BaseUtils |
BaseUtils contains some basic utilities for manipulating nucleotides.
|
| BinaryTableReader<R> |
Abstract base class for readers of table with records stored in binary.
|
| BinaryTableWriter<R> |
Abstract file writing class for record tables stored in binary format.
|
| ClassUtils |
Utilities for dealing with reflection.
|
| CompressedDataList<T> |
A class to represent data as a list of
|
| DigammaCache | |
| Dirichlet |
The Dirichlet distribution is a distribution on multinomial distributions: if pi is a vector of positive multinomial weights
such that sum_i pi[i] = 1, the Dirichlet pdf is P(pi) = [prod_i Gamma(alpha[i]) / Gamma(sum_i alpha[i])] * prod_i pi[i]^(alpha[i] - 1)
The vector alpha comprises the sufficient statistics for the Dirichlet distribution.
|
| FisherExactTest |
Implements the Fisher's exact test for 2x2 tables
assuming the null hypothesis of odd ratio of 1.
|
| GenomeLoc |
Genome location representation.
|
| GenomeLocParser |
Factory class for creating GenomeLocs
|
| GenomeLocSortedSet |
Class GenomeLocCollection
a set of genome locations.
|
| GenotypeCounts | |
| GenotypeUtils | |
| Histogram |
Class used for storing a list of doubles as a run length encoded histogram that compresses the data into bins spaced
at defined intervals.
|
| HttpUtils | |
| IGVUtils |
Utilities for interacting with IGV-specific formats.
|
| IndexRange |
Represents 0-based integer index range.
|
| IndexUtils | |
| IntegrationUtils |
Created by tsato on 5/1/17.
|
| IntervalUtils |
Parse text representations of interval strings that
can appear in GATK-based applications.
|
| IntToDoubleFunctionCache |
A helper class to maintain a cache of an int to double function defined on n = 0, 1, 2.
|
| KV<K,V> |
replacement for dataflow Key-Value class, don't use this anywhere new
|
| Log10Cache | |
| Log10FactorialCache |
Wrapper class so that the log10Factorial array is only calculated if it's used
|
| LoggingUtils |
Logging utilities.
|
| LRUCache<K,V> |
An LRU cache implemented as an extension to LinkedHashMap
|
| MannWhitneyU |
Imported with changes from Picard private.
|
| MannWhitneyU.RankedData |
The ranked data in one list and a list of the number of ties.
|
| MannWhitneyU.Result |
The results of performing a rank sum test.
|
| MannWhitneyU.TestStatistic |
The values of U1, U2 and the transformed number of ties needed for the calculation of sigma
in the normal approximation.
|
| MathUtils |
MathUtils is a static class (no instantiation allowed!) with some useful math methods.
|
| MathUtils.RunningAverage |
A utility class that computes on the fly average and standard deviation for a stream of numbers.
|
| MatrixSummaryUtils |
Static class for implementing some matrix summary stats that are not in Apache, Spark, etc
|
| NativeUtils |
Utilities to provide architecture-dependent native functions
|
| NaturalLogUtils | |
| Nucleotide.Counter |
Helper class to count the number of occurrences of each nucleotide code in
a sequence.
|
| OptimizationUtils |
Created by davidben on 4/27/16.
|
| QualityUtils |
QualityUtils is a static class with some utility methods for manipulating
quality scores.
|
| SATagBuilder |
A builder class that expands functionality for SA tags.
|
| SequenceDictionaryUtils |
A series of utility functions that enable the GATK to compare two sequence dictionaries -- from the reference,
from BAMs, or from feature sources -- for consistency.
|
| SimpleInterval |
Minimal immutable class representing a 1-based closed ended genomic interval
SimpleInterval does not allow null contig names.
|
| UniqueIDWrapper<A> |
Create a unique ID for an arbitrary object and wrap it.
|
| UnsignedTypeUtil |
A utility class for dealing with unsigned types.
|
| Utils | |
| ZipUtils |
Utility class to zip and unzip files.
|
| Enum | Description |
|---|---|
| BaseUtils.Base | |
| BaseUtils.BaseSubstitutionType | |
| GenomeLocParser.ValidationLevel |
How much validation should we do at runtime with this parser?
|
| IntervalMergingRule |
a class we use to determine the merging rules for intervals passed to the GATK
|
| IntervalSetRule |
set operators for combining lists of intervals
|
| IntervalUtils.IntervalBreakpointType |
An enum to classify breakpoints whether the breakpoint is the start or end of a region.
|
| MannWhitneyU.TestType |
A variable that indicates if the test is one sided or two sided and if it's one sided
which group is the dominator in the null hypothesis.
|
| NGSPlatform |
A canonical, master list of the standard NGS platforms.
|
| Nucleotide |
Represents the nucleotide alphabet with support for IUPAC ambiguity codes.
|
| SequenceDictionaryUtils.SequenceDictionaryCompatibility | |
| SequencerFlowClass |
In broad terms, each sequencing platform can be classified by whether it flows nucleotides in some order
such that homopolymers get sequenced in a single event (ie 454 or Ion) or it reads each position in the
sequence one at a time, regardless of base composition (Illumina or Solid).
|
| Tail |
Enum for two-sided things, for example which end of a read has been clipped, which end of a chain within an assembly graph etc.
|
| Trilean |
An enumeration to represent true, false, or unknown.
|