pileup

Type Members

1. case class Deletion(referenceBases: Seq[Byte], baseQuality: Byte) extends Alignment with Product with Serializable

   For now, only emit a Deletion at the position immediately preceding the run of deleted bases, i.

2. case class Insertion(sequencedBases: Seq[Byte], baseQualities: Seq[Byte]) extends Alignment with Product with Serializable

3. case class InvalidCigarElementException(elem: PileupElement) extends Exception with Product with Serializable

4. case class Match(base: Byte, baseQuality: Byte) extends MatchOrMisMatch with Product with Serializable

5. class MatchOrMisMatch extends Alignment

6. case class MidDeletion(referenceBase: Byte) extends Alignment with Product with Serializable

   Signifies that at a particular locus, a read has bases deleted.

7. case class Mismatch(base: Byte, baseQuality: Byte, referenceBase: Byte) extends MatchOrMisMatch with Product with Serializable

8. case class Pileup(sampleName: SampleName, contigName: ContigName, locus: Locus, contigSequence: ContigSequence, elements: Seq[PileupElement]) extends Product with Serializable

   A Pileup at a locus contains a sequence of PileupElement instances, one for every read that overlaps that locus.

9. case class PileupElement(read: MappedRead, locus: Locus, readPosition: Int, cigarElementIndex: Int, cigarElementLocus: Locus, indexWithinCigarElement: Int, contigSequence: ContigSequence) extends Product with Serializable

   A PileupElement represents the bases sequenced by a particular read at a particular reference locus.