org.bdgenomics.adam

# models

#### package models

Visibility

1. Public
2. All

### Type Members

1. #### trait Alphabet extends AnyRef

   Created by bryan on 4/17/15.

   Created by bryan on 4/17/15.

   An alphabet of symbols and related operations

2. #### case class Attribute(tag: String, tagType: TagType.Value, value: Any) extends Product with Serializable

   A wrapper around the attrTuple (key) and value pair.

   A wrapper around the attrTuple (key) and value pair. 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.

   Roughly analogous to Picards 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.

3. #### abstract class BlockExtractable extends Extractable

4. #### case class CDS(transcriptId: String, strand: Boolean, region: ReferenceRegion) extends BlockExtractable with Product with Serializable

   Coding Sequence annotations, should be a subset of an Exon for a particular Transcript

   Coding Sequence annotations, should be a subset of an Exon for a particular Transcript

   transcriptId
   strand
   region

5. #### case class Consensus(consensus: String, index: ReferenceRegion) extends Product with Serializable

6. #### class DNAAlphabet extends Alphabet

   The standard DNA alphabet with A,T,C, and G

7. #### case class Exon(exonId: String, transcriptId: String, strand: Boolean, region: ReferenceRegion) extends BlockExtractable with Product with Serializable

   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.

   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.

   NOTE: we're not handling shared exons here

   transcriptId

     the (unique) identifier of the transcript to which the exon belongs

   region

     The region (in genomic coordinates) to which the exon maps

8. #### trait Extractable extends AnyRef

   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 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. Passing the sequence of the reference chromosome to a transcript's 'extractSequence' method will return the sequence of the transcript.

9. #### case class Gene(id: String, names: Seq[String], strand: Boolean, transcripts: Iterable[Transcript]) extends Product with Serializable

   A 'gene model' is a small, hierarchical collection of objects: Genes, Transcripts, and Exons.

   A 'gene model' is a small, hierarchical collection of objects: Genes, Transcripts, and Exons. Each Gene contains a collection of Transcripts, and each Transcript contains a collection of Exons, and together they describe how the genome is transcribed and translated into a family of related proteins (or other RNA products that aren't translated at all).

   This review, Gerstein et al. "What is a gene, post-ENCODE? History and updated definition" Genome Research (2007) http://genome.cshlp.org/content/17/6/669.full

   is a reasonably good overview both of what the term 'gene' has meant in the past as well as where it might be headed in the future.

   Here, we aren't trying to answer any of these questions about "what is a gene," but rather to provide the routines necessary to _re-assemble_ hierarchical models of genes that have been flattened into features (GFF, GTF, or BED)

   id

     A name, presumably unique within a gene dataset, of a Gene

   names

     Common names for the gene, possibly shared with other genes (for historical or ad hoc reasons)

   strand

     The strand of the Gene (this is from data, not derived from the Transcripts' strand(s), and we leave open the possibility that a single Gene will have Transcripts in _both_ directions, e.g. anti-sense transcripts)

   transcripts

     The Transcripts that are part of this gene model

10. #### class IndelTable extends Serializable with Logging

11. #### trait Interval extends AnyRef

    An interval is a region on a coordinate space that has a defined width.

    An interval is a region on a coordinate space that has a defined width. This can be used to express a region of a genome, a transcript, a gene, etc.

12. #### class MultiContigNonoverlappingRegions extends Serializable

    Creates a multi-reference-region collection of NonoverlappingRegions -- see the scaladocs to NonoverlappingRegions.

13. #### class NonoverlappingRegions extends Serializable

    The evaluation of a regionJoin takes place with respect to a complete partition on the total space of the genome.

    The evaluation of a regionJoin takes place with respect to a complete partition on the total space of the genome. NonoverlappingRegions is a class to compute the value of that partition, and to allow us to assign one or more elements of that partition to a new ReferenceRegion (see the 'regionsFor' method).

    NonoverlappingRegions takes, as input, and 'input-set' of regions. These are arbitrary ReferenceRegions, which may be overlapping, identical, disjoint, etc. The input-set of regions _must_ all be located on the same reference chromosome (i.e. must all have the same refName); the generalization to reference regions from multiple chromosomes is in MultiContigNonoverlappingRegions, below.

    NonoverlappingRegions produces, internally, a 'nonoverlapping-set' of regions. This is basically the set of _distinct unions_ of the input-set regions.

14. #### trait OptionalReferenceOrdering[T <: ReferenceRegion] extends Ordering[Option[T]]

15. #### case class ProgramRecord(id: String, commandLine: Option[String], name: Option[String], version: Option[String], previousID: Option[String]) extends Product with Serializable

16. #### case class ReadBucket(unpairedPrimaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedFirstPrimaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedSecondPrimaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, unpairedSecondaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedFirstSecondaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedSecondSecondaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, unmappedReads: Iterable[AlignmentRecord] = Seq.empty) extends Product with Serializable

    This class is similar to SingleReadBucket, except it breaks the reads down further.

    This class is similar to SingleReadBucket, except it breaks the reads down further.

    Rather than stopping at primary/secondary/unmapped, this will break it down further into whether they are paired or unpaired, and then whether they are the first or second of the pair.

    This is useful as this will usually map a single read in any of the sequences.

17. #### class ReadBucketSerializer extends Serializer[ReadBucket]

18. #### class RecordGroup extends Serializable

19. #### class RecordGroupDictionary extends Serializable

    Builds a dictionary containing record groups.

    Builds a dictionary containing record groups. Record 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.

    Exceptions thrown
      AssertionError

      Throws an assertion error if there are multiple record groups with the same name.

20. #### trait ReferenceOrdering[T <: ReferenceRegion] extends Ordering[T]

21. #### class ReferencePosition extends ReferenceRegion

22. #### case class ReferencePositionPair(read1refPos: Option[ReferencePosition], read2refPos: Option[ReferencePosition]) extends Product with Serializable

23. #### class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

24. #### class ReferencePositionSerializer extends Serializer[ReferencePosition]

25. #### case class ReferenceRegion(referenceName: String, start: Long, end: Long, orientation: Strand = Strand.Independent) extends Comparable[ReferenceRegion] with Interval 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.

26. #### class ReferenceRegionSerializer extends Serializer[ReferenceRegion]

27. #### class SAMFileHeaderWritable extends Serializable

28. #### class SequenceDictionary extends Serializable

29. #### 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], referenceIndex: Option[Int]) extends Serializable with Product

    Utility class within the SequenceDictionary; represents unique reference name-to-id correspondence

30. #### case class SingleReadBucket(primaryMapped: Iterable[AlignmentRecord] = Seq.empty, secondaryMapped: Iterable[AlignmentRecord] = Seq.empty, unmapped: Iterable[AlignmentRecord] = Seq.empty) extends Product with Serializable

31. #### class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

32. #### class SnpTable extends Serializable with Logging

33. #### 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

34. #### case class Transcript(id: String, names: Seq[String], geneId: String, strand: Boolean, exons: Iterable[Exon], cds: Iterable[CDS], utrs: Iterable[UTR]) extends Product with Serializable

    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).

    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).

    id

      the (unique) identifier of the Transcript

    names

      Common names for the transcript

    geneId

      The (unique) identifier of the gene to which the transcript belongs

    exons

      The set of exons in the transcript model; each of these contain a reference region whose coordinates are in genomic space.

    cds

      the set of CDS regions (the subset of the exons that are coding) for this transcript

    utrs

35. #### case class UTR(transcriptId: String, strand: Boolean, region: ReferenceRegion) extends BlockExtractable with Product with Serializable

    UnTranslated Regions

    UnTranslated Regions

    transcriptId
    strand
    region

36. #### case class VCFHeaderWritable(header: VCFHeader) extends Product with Serializable

37. #### class VariantContext extends AnyRef

### Value Members

1. #### object Alphabet

2. #### object Consensus extends Serializable

3. #### object IndelTable extends Serializable

4. #### object MultiContigNonoverlappingRegions extends Serializable

5. #### object NonoverlappingRegions extends Serializable

6. #### object OptionalPositionOrdering extends OptionalReferenceOrdering[ReferencePosition]

7. #### object OptionalRegionOrdering extends OptionalReferenceOrdering[ReferenceRegion]

8. #### object PositionOrdering extends ReferenceOrdering[ReferencePosition]

9. #### object ProgramRecord extends Serializable

10. #### object ReadBucket extends Serializable

11. #### object RecordGroup extends Serializable

12. #### object RecordGroupDictionary extends Serializable

13. #### object ReferencePosition extends Serializable

14. #### object ReferencePositionPair extends Logging with Serializable

15. #### object ReferenceRegion extends Serializable

16. #### object ReferenceUtils

17. #### object RegionOrdering extends ReferenceOrdering[ReferenceRegion]

18. #### object SAMFileHeaderWritable extends Serializable

19. #### object SequenceDictionary extends Serializable

    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.

20. #### object SequenceOrderingByName extends Ordering[SequenceRecord]

21. #### object SequenceOrderingByRefIdx extends Ordering[SequenceRecord]

22. #### object SequenceRecord extends Serializable

23. #### object SingleReadBucket extends Logging with Serializable

24. #### object SnpTable extends Serializable

25. #### object TagType extends Enumeration

26. #### object VariantContext

    Note: VariantContext inherits its name from the Picard VariantContext, and is not related to the SparkContext object.

    Note: VariantContext inherits its name from the Picard VariantContext, and is not related to the SparkContext object. If you're looking for the latter, see org.bdgenomics.adam.rdd.variation.VariationContext

### Ungrouped