models
An alphabet of symbols and related operations
A wrapper around the attrTuple (key) and value pair seen in many formats.
Coverage record for CoverageDataset.
Coverage record for CoverageDataset.
Contains Region indexed by reference name, start and end, as well as the average coverage at each base pair in that region.
The chromosome that this coverage was observed on.
The start coordinate of the region where this coverage value was observed.
The end coordinate of the region where this coverage value was observed.
The average coverage across this region.
Option of sampleId for this Coverage record
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.
Represents the mismatches and deletions present in a read that has been aligned to a reference genome. The MD tag can be used to reconstruct the reference that an aligned read overlaps.
Start position of the alignment.
A list of the ranges over which the read has a perfect sequence match.
A map of all the locations where a base mismatched.
A map of all locations where a base was deleted.
A read group represents a set of reads that were sequenced/processed/prepped/analyzed together.
A read group represents a set of reads that were sequenced/processed/prepped/analyzed together.
The sample these reads are from.
The identifier for this read group.
The optional name of the place where these reads were sequenced.
An optional description for this read group.
An optional Unix epoch timestamp for when these reads were run through the sequencer.
An optional string of nucleotides that were used for each flow of each read.
An optional string of nucleotides that are the key for this read.
An optional library name.
An optional prediction of the read insert size for this library prep.
An optional description for the platform this group was sequenced on.
An optional ID for the sequencer this group was sequenced on.
Builds a dictionary containing read groups.
Builds a dictionary containing read groups.
Read groups must have a unique name across all samples in the dictionary. This dictionary provides numerical IDs for each group; these IDs are only consistent when referencing a single dictionary.
A seq of read groups to populate the dictionary.
IllegalArgumentException Throws an assertion error if there are multiple read
groups with the same name.
A single genomic locus.
Represents a contiguous region of the reference genome.
Represents a contiguous region of the reference genome.
The name of the sequence (chromosome) in the reference genome
The 0-based residue-coordinate for the start of the region
The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e. [start, end) define a 0-based half-open interval.
The strand of the genome that this region exists on.
A SequenceDictionary contains metadata about the reference build genomic data is aligned against.
A SequenceDictionary contains metadata about the reference build genomic data is aligned against.
SequenceRecord
Metadata about a single reference sequence.
Metadata about a single reference sequence.
The name of this reference in the assembly.
The length of the sequence for this reference.
If available, the URI from which the reference sequence was obtained.
If available, the MD5 checksum uniquely representing this reference as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (equivalent to SQ:M5 in SAM).
If available, the REFSEQ ID for the reference.
If available, the Genbank ID for the reference.
If available, the name of the assembly for this reference.
If available, the species that this reference is for.
If available, the number of this reference in a set of references.
A table containing all of the SNPs in a known variation dataset.
A symbol in an alphabet.
A symbol in an alphabet.
a character which represents the symbol
acharacter which represents the complement of the symbol
A representation of all variation data at a single variant.
A representation of all variation data at a single variant.
This class represents an equivalent to a single allele from a VCF line, and is the ADAM equivalent to htsjdk.variant.variantcontext.VariantContext.
Singleton object with references to all supported alphabets.
Companion object to MdTag case class.
Companion object to MdTag case class. Provides methods for building an MdTag model from a read.
Enumeration describing sequence events in an MD tag:
Enumeration describing sequence events in an MD tag:
* Match is a sequence match (i.e., every base in the aligned sequence matches the reference sequence) * Mismatch is a sequence mismatch (there are bases that do not match the reference sequence) * Delete indicates that bases that were present in the reference sequence were deleted in the read sequence
A sort order that orders all given positions lexicographically by reference and numerically within a single reference, and puts all non-provided positions at the end.
A sort order that orders all given positions lexicographically by reference and numerically within a single reference, and puts all non-provided positions at the end. An extension of PositionOrdering to Optional data.
PositionOrdering
A sort order that orders all given regions lexicographically by reference and numerically within a single reference sequence, and puts all non-provided regions at the end.
A sort order that orders all given regions lexicographically by reference and numerically within a single reference sequence, and puts all non-provided regions at the end. An extension of PositionOrdering to Optional data.
PositionOrdering
A sort order that orders all positions lexicographically by reference and numerically within a single reference.
Singleton object for creating ReaGroups.
Singleton object for creating dictionaries of read 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 reference and numerically within a single reference sequence, and puts all non-provided regions at the end.
A sort order that orders all given regions lexicographically by reference and numerically within a single reference sequence, and puts all non-provided regions at the end. Regions are compared by start position first. If start positions are equal, then we compare by end position.
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.
A wrapper around the attrTuple (key) and value pair seen in many formats.
Includes the attrTuple-type explicitly, rather than embedding the corresponding information in the type of 'value', because otherwise it'd be difficult to extract the correct type for Byte and NumericSequence values.
This class is roughly analogous to htsjdk's SAMTagAndValue.
The string key associated with this pair.
An enumerated value representing the type of the 'value' parameter.
The 'value' half of the pair.