models

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