org.bdgenomics.adam

# models

#### package models

Visibility

1. Public
2. All

### Type Members

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

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

2. #### class BEDFeature extends BaseFeature

3. #### class BaseFeature extends Serializable

4. #### abstract class BlockExtractable extends Extractable

5. #### 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

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

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. #### class GTFFeature extends BaseFeature

10. #### 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.

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

12. #### trait Interval extends AnyRef

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

13. #### class NarrowPeakFeature extends BaseFeature

    See: http://genome.

14. #### class OrderedTrackedLayout [T] extends TrackedLayout[T]

    An implementation of TrackedLayout which takes a sequence of ReferenceMappable values, and lays them out in order (i.

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 ReferenceMapping [T] extends AnyRef

21. #### case class ReferencePosition (referenceName: String, pos: Long) extends Ordered[ReferencePosition] with Product with Serializable

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

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

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

25. #### case class ReferencePositionWithOrientation (refPos: ReferencePosition, negativeStrand: Boolean) extends Ordered[ReferencePositionWithOrientation] with Product with Serializable

26. #### class ReferencePositionWithOrientationSerializer extends Serializer[ReferencePositionWithOrientation]

27. #### case class ReferenceRegion (referenceName: String, start: Long, end: Long) extends Ordered[ReferenceRegion] with Interval with Product with Serializable

    Represents a contiguous region of the reference genome.

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

29. #### case class ReferenceRegionWithOrientation (region: ReferenceRegion, negativeStrand: Boolean) extends Ordered[ReferenceRegionWithOrientation] with Product with Serializable

    Represents a contiguous region of the reference genome with strand information.

30. #### case class Rod (position: ReferencePosition, pileups: List[Pileup]) extends Product with Serializable

    Class representing a set of pileup bases at a specific locus.

31. #### class SAMFileHeaderWritable extends Serializable

32. #### class SequenceDictionary extends Serializable

33. #### class SequenceRecord extends Serializable

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

34. #### 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

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

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

37. #### trait TrackedLayout [T] extends AnyRef

    A TrackedLayout is an assignment of values of some type T (which presumably are mappable to a reference genome or other linear coordinate space) to 'tracks' -- that is, to integers, with the guarantee that no two values assigned to the same track will overlap.

38. #### 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).

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

    UnTranslated Regions

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

41. #### class VariantContext extends AnyRef

### Value Members

1. #### object BEDFeature extends Serializable

2. #### object BaseFeature extends Serializable

3. #### object Consensus extends Serializable

4. #### object IndelTable extends Serializable

5. #### object ProgramRecord extends Serializable

6. #### object ReadBucket extends Serializable

7. #### object RecordGroup extends Serializable

8. #### object RecordGroupDictionary extends Serializable

9. #### object ReferencePosition extends Serializable

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

11. #### object ReferencePositionWithOrientation extends Serializable

12. #### object ReferenceRegion extends Serializable

13. #### object ReferenceRegionWithOrientation extends Serializable

14. #### object ReferenceUtils

15. #### object SAMFileHeaderWritable extends Serializable

16. #### 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.

17. #### object SequenceRecord extends Serializable

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

19. #### object SnpTable extends Serializable

20. #### object TagType extends Enumeration

21. #### object TrackedLayout

22. #### object VariantContext

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

### Ungrouped