models

Type Members

1. case class ADAMRod(position: ReferencePosition, pileups: List[ADAMPileup]) extends Product with Serializable

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

2. class ADAMVariantContext extends AnyRef

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

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

4. class BEDFeature extends BaseFeature

5. class BaseFeature extends AnyRef

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

7. class IndelTable extends Serializable with Logging

8. class NarrowPeakFeature extends BaseFeature

9. case class ReadBucket(unpairedPrimaryMappedReads: Iterable[ADAMRecord] = collection.this.Seq.empty[Nothing], pairedFirstPrimaryMappedReads: Iterable[ADAMRecord] = collection.this.Seq.empty[Nothing], pairedSecondPrimaryMappedReads: Iterable[ADAMRecord] = collection.this.Seq.empty[Nothing], unpairedSecondaryMappedReads: Iterable[ADAMRecord] = collection.this.Seq.empty[Nothing], pairedFirstSecondaryMappedReads: Iterable[ADAMRecord] = collection.this.Seq.empty[Nothing], pairedSecondSecondaryMappedReads: Iterable[ADAMRecord] = collection.this.Seq.empty[Nothing], unmappedReads: Iterable[ADAMRecord] = 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 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 SAMFileHeaderWritable(header: SAMFileHeader) extends Serializable with Product

24. class SequenceDictionary extends Serializable

25. class SequenceRecord extends Serializable

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

26. case class SingleReadBucket(primaryMapped: Iterable[ADAMRecord] = collection.this.Seq.empty[Nothing], secondaryMapped: Iterable[ADAMRecord] = collection.this.Seq.empty[Nothing], unmapped: Iterable[ADAMRecord] = collection.this.Seq.empty[Nothing]) extends Product with Serializable

27. class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

28. class SnpTable extends Serializable with Logging