Created by bryan on 4/17/15.
A wrapper around the attrTuple (key) and value pair.
Coding Sequence annotations, should be a subset of an Exon for a particular Transcript
The standard DNA alphabet with A,T,C, and G
An exon model (here represented as a value of the Exon class) is a representation of a single exon from a transcript in genomic coordinates.
A trait for values (usually regions or collections of regions) that can be subsetted or extracted out of a larger region string -- for example, exons or transcripts which have a sequence defined in terms of their coordinates against a reference chromosome.
A 'gene model' is a small, hierarchical collection of objects: Genes, Transcripts, and Exons.
An interval is a region on a coordinate space that has a defined width.
Creates a multi-reference-region collection of NonoverlappingRegions -- see the scaladocs to NonoverlappingRegions.
The evaluation of a regionJoin takes place with respect to a complete partition on the total space of the genome.
This class is similar to SingleReadBucket, except it breaks the reads down further.
Builds a dictionary containing record groups.
Represents a contiguous region of the reference genome.
Utility class within the SequenceDictionary; represents unique reference name-to-id correspondence
A symbol in an alphabet
A transcript model (here represented as a value of the Transcript class) is a simple, hierarchical model containing a collection of exon models as well as an associated gene identifier, transcript identifier, and a set of common names (synonyms).
UnTranslated Regions
SequenceDictionary contains the (bijective) map between Ints (the referenceId) and Strings (the referenceName) from the header of a BAM file, or the combined result of multiple such SequenceDictionaries.
Note: VariantContext inherits its name from the Picard VariantContext, and is not related to the SparkContext object.