package models
- Alphabetic
- Public
- All
Type Members
-
trait
Alphabet extends AnyRef
An alphabet of symbols and related operations
-
case class
Attribute(tag: String, tagType: TagType.Value, value: Any) extends Product with Serializable
A wrapper around the attrTuple (key) and value pair seen in many formats.
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.
- tag
The string key associated with this pair.
- tagType
An enumerated value representing the type of the 'value' parameter.
- value
The 'value' half of the pair.
-
case class
Coverage(referenceName: String, start: Long, end: Long, count: Double, optSampleId: Option[String] = None) extends Product with Serializable
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.
- referenceName
The chromosome that this coverage was observed on.
- start
The start coordinate of the region where this coverage value was observed.
- end
The end coordinate of the region where this coverage value was observed.
- count
The average coverage across this region.
- optSampleId
Option of sampleId for this Coverage record
-
class
DNAAlphabet extends Alphabet
The standard DNA alphabet with A,T,C, and G.
-
class
IUPACAlphabet extends Alphabet
The IUPAC amino acid and nucleotide base alphabet with ambiguity codes.
-
case class
MdTag(start: Long, matches: List[NumericRange[Long]], mismatches: Map[Long, Char], deletions: Map[Long, Char]) extends Product with Serializable
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
Start position of the alignment.
- matches
A list of the ranges over which the read has a perfect sequence match.
- mismatches
A map of all the locations where a base mismatched.
- deletions
A map of all locations where a base was deleted.
- trait OptionalReferenceOrdering[T <: ReferenceRegion] extends Ordering[Option[T]]
-
case class
ReadGroup(sampleId: String, id: String, sequencingCenter: Option[String] = None, description: Option[String] = None, runDateEpoch: Option[Long] = None, flowOrder: Option[String] = None, keySequence: Option[String] = None, library: Option[String] = None, predictedMedianInsertSize: Option[Int] = None, platform: Option[String] = None, platformUnit: Option[String] = None) extends Product with Serializable
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.
- sampleId
The sample these reads are from.
- id
The identifier for this read group.
- sequencingCenter
The optional name of the place where these reads were sequenced.
- description
An optional description for this read group.
- runDateEpoch
An optional Unix epoch timestamp for when these reads were run through the sequencer.
- flowOrder
An optional string of nucleotides that were used for each flow of each read.
- keySequence
An optional string of nucleotides that are the key for this read.
- library
An optional library name.
- predictedMedianInsertSize
An optional prediction of the read insert size for this library prep.
- platform
An optional description for the platform this group was sequenced on.
- platformUnit
An optional ID for the sequencer this group was sequenced on.
-
case class
ReadGroupDictionary(readGroups: Seq[ReadGroup]) extends Product with Serializable
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.
- readGroups
A seq of read groups to populate the dictionary.
- Exceptions thrown
IllegalArgumentException
Throws an assertion error if there are multiple read groups with the same name.
- trait ReferenceOrdering[T <: ReferenceRegion] extends Ordering[T]
-
class
ReferencePosition extends ReferenceRegion
A single genomic locus.
- class ReferencePositionSerializer extends Serializer[ReferencePosition]
-
case class
ReferenceRegion(referenceName: String, start: Long, end: Long, strand: Strand = Strand.INDEPENDENT) extends Comparable[ReferenceRegion] with Interval[ReferenceRegion] with Product with Serializable
Represents a contiguous region of the reference genome.
Represents a contiguous region of the reference genome.
- referenceName
The name of the sequence (chromosome) in the reference genome
- start
The 0-based residue-coordinate for the start of the region
- end
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.
- strand
The strand of the genome that this region exists on.
- class ReferenceRegionSerializer extends Serializer[ReferenceRegion]
-
class
SequenceDictionary extends Serializable
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.
- See also
SequenceRecord
-
case class
SequenceRecord(name: String, length: Long, url: Option[String], md5: Option[String], refseq: Option[String], genbank: Option[String], assembly: Option[String], species: Option[String], index: Option[Int]) extends Serializable with Product
Metadata about a single reference sequence.
Metadata about a single reference sequence.
- name
The name of this reference in the assembly.
- length
The length of the sequence for this reference.
- url
If available, the URI from which the reference sequence was obtained.
- md5
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).
- refseq
If available, the REFSEQ ID for the reference.
- genbank
If available, the Genbank ID for the reference.
- assembly
If available, the name of the assembly for this reference.
- species
If available, the species that this reference is for.
- index
If available, the number of this reference in a set of references.
-
class
SnpTable extends Serializable
A table containing all of the SNPs in a known variation dataset.
-
case class
Symbol(label: Char, complement: Char) extends Product with Serializable
A symbol in an alphabet.
A symbol in an alphabet.
- label
a character which represents the symbol
- complement
acharacter which represents the complement of the symbol
-
class
VariantContext extends Serializable
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.
- class VariantContextSerializer extends Serializer[VariantContext]
Value Members
-
object
Alphabet
Singleton object with references to all supported alphabets.
-
object
MdTag extends Serializable
Companion object to MdTag case class.
Companion object to MdTag case class. Provides methods for building an MdTag model from a read.
-
object
MdTagEvent extends Enumeration
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
-
object
OptionalPositionOrdering extends OptionalReferenceOrdering[ReferencePosition]
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.
- See also
PositionOrdering
-
object
OptionalRegionOrdering extends OptionalReferenceOrdering[ReferenceRegion]
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.
- See also
PositionOrdering
-
object
PositionOrdering extends ReferenceOrdering[ReferencePosition]
A sort order that orders all positions lexicographically by reference and numerically within a single reference.
-
object
ReadGroup extends Serializable
Singleton object for creating ReaGroups.
-
object
ReadGroupDictionary extends Serializable
Singleton object for creating dictionaries of read groups.
-
object
ReferencePosition extends Serializable
Companion object for creating and sorting ReferencePositions.
-
object
ReferenceRegion extends Serializable
A companion object for creating and ordering ReferenceRegions.
-
object
RegionOrdering extends ReferenceOrdering[ReferenceRegion]
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.
-
object
SequenceDictionary extends Serializable
Singleton object for creating SequenceDictionaries.
-
object
SequenceRecord extends Serializable
Companion object for creating Sequence Records.
-
object
SnpTable extends Serializable
Companion object with helper functions for building SNP tables.
-
object
TagType extends Enumeration
An enumeration that describes the different data types that can be stored in an attribute.
-
object
VariantContext extends Serializable
Singleton object for building VariantContexts.