reads

Type Members

1. case class MappedRead(name: String, sequence: Bases, baseQualities: IndexedSeq[Byte], isDuplicate: Boolean, contigName: ContigName, alignmentQuality: Int, start: Locus, cigar: Cigar, failedVendorQualityChecks: Boolean, isPositiveStrand: Boolean, isPaired: Boolean) extends Read with Region with Product with Serializable

   A mapped read.

2. class MappedReadSerializer extends Serializer[MappedRead]

3. case class MateAlignmentProperties(contigName: ContigName, start: Locus, inferredInsertSize: Option[Int], isPositiveStrand: Boolean) extends Product with Serializable

   Details of the mate read alignment

4. case class PairedRead[+T <: Read](read: T, isFirstInPair: Boolean, mateAlignmentProperties: Option[MateAlignmentProperties]) extends Read with Product with Serializable

   PairedRead is a MappedRead or UnmappedRead with the additional mate information

5. trait Read extends AnyRef

   The fields in the Read trait are common to any read, whether mapped (aligned) or not.

6. class Registrar extends KryoRegistrator

7. case class UnmappedRead(name: String, sequence: Bases, baseQualities: IndexedSeq[Byte], isDuplicate: Boolean, failedVendorQualityChecks: Boolean, isPaired: Boolean) extends Read with Product with Serializable

   An unmapped read.

8. class UnmappedReadSerializer extends Serializer[UnmappedRead]