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.

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

   A wrapper around the attrTuple (key) and value 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

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.

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.

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.

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.

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.

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] = collection.this.Seq.empty[Nothing], pairedFirstPrimaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedSecondPrimaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], unpairedSecondaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedFirstSecondaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedSecondSecondaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], unmappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing]) extends Product with Serializable

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

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

18. #### class RecordGroup extends Serializable

19. #### class RecordGroupDictionary extends Serializable

    Builds a dictionary containing record groups.

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 = ...) extends Comparable[ReferenceRegion] with Interval with Product with Serializable

    Represents a contiguous region of the reference genome.

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] = collection.this.Seq.empty[Nothing], secondaryMapped: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], unmapped: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing]) 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

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).

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

    UnTranslated Regions

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.

### Ungrouped