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. case class Consensus(consensus: String, index: NumericRange[Long]) extends Product with Serializable

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

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

6. class ReadBucketSerializer extends Serializer[ReadBucket]

7. class RecordGroupDictionary extends Serializable

8. trait ReferenceMapping[T] extends AnyRef

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

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

11. class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

12. class ReferencePositionSerializer extends Serializer[ReferencePosition]

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

14. class ReferencePositionWithOrientationSerializer extends Serializer[ReferencePositionWithOrientation]

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

    Represents a contiguous region of the reference genome.

16. class ReferenceRegionSerializer extends Serializer[ReferenceRegion]

17. class 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.

18. class SequenceRecord extends Serializable

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

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

20. class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

21. class SnpTable extends Serializable with Logging