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.

   A mapped read. See the Read trait for some of the field descriptions.

   contigName

   the contig name (e.g. "chr12") that this read was mapped to.

   alignmentQuality

   the mapping quality, phred scaled.

   start

   the (0-based) reference locus that the first base in this read aligns to.

   cigar

   parsed samtools CIGAR object.

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

   Details of the mate read alignment

   contigName

   Contig/chromosome of the mate read

   start

   0-based start position of the mate read

   inferredInsertSize

   Insert size between the reads if defined

   isPositiveStrand

   Whether the mate is on the positive strand

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

   PairedRead is a MappedRead or UnmappedRead with the additional mate information

   T

   UnmappedRead or MappedRead

   read

   Unmapped or MappedRead base read

   isFirstInPair

   Whether the read is earlier that the the mate read

   mateAlignmentProperties

   Alignment location of the mate if it the mate is aligned

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.

   An unmapped read. See the Read trait for field descriptions.

8. class UnmappedReadSerializer extends Serializer[UnmappedRead]