models

Type Members

1. case class Clipped(size: Int, soft: Boolean = true) extends ObservationOperator with Product with Serializable

   A block representing bases clipped from the read.

2. case class Deletion(basesDeleted: String) extends ObservationOperator with Product with Serializable

   A block representing a deletion from the reference.

3. case class Insertion(size: Int) extends ObservationOperator with Product with Serializable

   A block representing an insertion into the reference.

4. case class Match(size: Int, optMismatchingBases: Option[String] = scala.None) extends ObservationOperator with Product with Serializable

   An alignment match block (M), further broken down into a sequence (mis)match.

5. case class Observation(alleleForwardStrand: Int, otherForwardStrand: Int, squareMapQ: Double, referenceLogLikelihoods: Array[Double], alleleLogLikelihoods: Array[Double], otherLogLikelihoods: Array[Double], nonRefLogLikelihoods: Array[Double], alleleCoverage: Int, otherCoverage: Int, totalCoverage: Int, isRef: Boolean, copyNumber: Int) extends Product with Serializable

   A generic class that stores likelihoods and simple annotations.

6. sealed trait ObservationOperator extends AnyRef

   A trait that implements an alignment operator.