An alphabet of symbols and related operations
A wrapper around the attrTuple (key) and value pair seen in many formats.
Coverage record for CoverageRDD.
The standard DNA alphabet with A,T,C, and G
Represents the mismatches and deletions present in a read that has been aligned to a reference genome.
A record group represents a set of reads that were sequenced/processed/prepped/analyzed together.
Builds a dictionary containing record groups.
A single genomic locus.
Represents a contiguous region of the reference genome.
A SequenceDictionary contains metadata about the reference build genomic data is aligned against.
Metadata about a single reference contig.
A table containing all of the SNPs in a known variation dataset.
A symbol in an alphabet.
A representation of all variation data at a single variant.
Singleton object with references to all supported alphabets.
Companion object to MdTag case class.
Enumeration describing sequence events in an MD tag:
A sort order that orders all given positions lexicographically by contig and numerically within a single contig, and puts all non-provided positions at the end.
A sort order that orders all given regions lexicographically by contig and numerically within a single contig, and puts all non-provided regions at the end.
A sort order that orders all positions lexicographically by contig and numerically within a single contig.
Singleton object for creating RecordGroups.
Singleton object for creating dictionaries of record groups.
Companion object for creating and sorting ReferencePositions.
A companion object for creating and ordering ReferenceRegions.
A sort order that orders all given regions lexicographically by contig and numerically within a single contig, and puts all non-provided regions at the end.
Singleton object for creating SequenceDictionaries.
Companion object for creating Sequence Records.
Companion object with helper functions for building SNP tables.
An enumeration that describes the different data types that can be stored in an attribute.
Singleton object for building VariantContexts.