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 AnyRef

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

5. class IndelTable extends Serializable with Logging

6. trait Interval extends AnyRef

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

7. class NarrowPeakFeature extends BaseFeature

8. class OrderedTrackedLayout[T] extends TrackedLayout[T]

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

9. 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.

10. class ReadBucketSerializer extends Serializer[ReadBucket]

11. class RecordGroup extends Serializable

12. class RecordGroupDictionary extends Serializable

    Builds a dictionary containing record groups.

13. trait ReferenceMapping[T] extends AnyRef

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

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

16. class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

17. class ReferencePositionSerializer extends Serializer[ReferencePosition]

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

19. class ReferencePositionWithOrientationSerializer extends Serializer[ReferencePositionWithOrientation]

20. 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.

21. class ReferenceRegionSerializer extends Serializer[ReferenceRegion]

22. case class ReferenceRegionWithOrientation(referenceName: String, start: Long, end: Long, negativeStrand: Boolean) extends Ordered[ReferenceRegionWithOrientation] with Product with Serializable

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

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

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

24. case class SAMFileHeaderWritable(header: SAMFileHeader) extends Serializable with Product

25. class SequenceDictionary extends Serializable

26. class SequenceRecord extends Serializable

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

27. 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

28. class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

29. class SnpTable extends Serializable with Logging

30. 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.

31. class VariantContext extends AnyRef