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.

   A block representing bases clipped from the read.

   size

   The number of bases clipped.

   soft

   True if soft clipped, false if hard clipped.

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

   

   A block representing a deletion from the reference.

   A block representing a deletion from the reference.

   basesDeleted

   The bases deleted from the reference.

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

   

   A block representing an insertion into the reference.

   A block representing an insertion into the reference.

   size

   The insertion length.

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

   

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

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

   size

   The size of this block.

   optMismatchingBases

   If this block is a sequence match (=), this will be empty. If this block is a sequence mismatch (X), this will contain the mismatching reference bases.

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.

   A generic class that stores likelihoods and simple annotations.

   alleleForwardStrand

   The number of reads covering the allele observed on the forward strand.

   otherForwardStrand

   The number of reads covering the site but not matching the allele observed on the forward strand.

   squareMapQ

   The sum of the squares of the mapping qualities observed.

   referenceLogLikelihoods

   The log likelihoods that 0...n copies of the reference allele were observed.

   alleleLogLikelihoods

   The log likelihoods that 0...n copies of this allele were observed.

   otherLogLikelihoods

   The log likelihoods that 0...n copies of an unknown allele were observed.

   alleleCoverage

   The total number of reads observed that cover the site and match the allele.

   otherCoverage

   The total number of reads observed that cover the site but that do not match the allele.

   totalCoverage

   The total number of reads that cover the site.

   isRef

   True if this allele matches the reference.

6. sealed trait ObservationOperator extends AnyRef

   

   A trait that implements an alignment operator.

   A trait that implements an alignment operator.

   These operators represent a limited subset of the CIGAR operators:

   * Alignment Match (M --> X/=) * Insertion (I) * Deletion (D) * Clip (S/H)