reads

Type Members

1. trait HasSampleId extends AnyRef

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

   A mapped read.

3. class MappedReadSerializer extends Serializer[MappedRead]

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

   Details of the mate read alignment

5. 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

6. trait Read extends HasSampleId

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

7. type SampleRegion = ReferenceRegion with HasSampleId

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

   An unmapped read.

9. class UnmappedReadSerializer extends Serializer[UnmappedRead]