case class ReadGroup(sampleId: String, id: String, sequencingCenter: Option[String] = None, description: Option[String] = None, runDateEpoch: Option[Long] = None, flowOrder: Option[String] = None, keySequence: Option[String] = None, library: Option[String] = None, predictedMedianInsertSize: Option[Int] = None, platform: Option[String] = None, platformUnit: Option[String] = None) extends Product with Serializable

A read group represents a set of reads that were sequenced/processed/prepped/analyzed together.

sampleId

The sample these reads are from.

id

The identifier for this read group.

sequencingCenter

The optional name of the place where these reads were sequenced.

description

An optional description for this read group.

runDateEpoch

An optional Unix epoch timestamp for when these reads were run through the sequencer.

flowOrder

An optional string of nucleotides that were used for each flow of each read.

keySequence

An optional string of nucleotides that are the key for this read.

library

An optional library name.

predictedMedianInsertSize

An optional prediction of the read insert size for this library prep.

platform

An optional description for the platform this group was sequenced on.

platformUnit

An optional ID for the sequencer this group was sequenced on.

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  1. ReadGroup
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Instance Constructors

  1. new ReadGroup(sampleId: String, id: String, sequencingCenter: Option[String] = None, description: Option[String] = None, runDateEpoch: Option[Long] = None, flowOrder: Option[String] = None, keySequence: Option[String] = None, library: Option[String] = None, predictedMedianInsertSize: Option[Int] = None, platform: Option[String] = None, platformUnit: Option[String] = None)

    sampleId

    The sample these reads are from.

    id

    The identifier for this read group.

    sequencingCenter

    The optional name of the place where these reads were sequenced.

    description

    An optional description for this read group.

    runDateEpoch

    An optional Unix epoch timestamp for when these reads were run through the sequencer.

    flowOrder

    An optional string of nucleotides that were used for each flow of each read.

    keySequence

    An optional string of nucleotides that are the key for this read.

    library

    An optional library name.

    predictedMedianInsertSize

    An optional prediction of the read insert size for this library prep.

    platform

    An optional description for the platform this group was sequenced on.

    platformUnit

    An optional ID for the sequencer this group was sequenced on.

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  6. val description: Option[String]
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(o: Any): Boolean

    Compares equality to another object.

    Compares equality to another object. Only checks equality via the sampleId and id fields.

    o

    Object to compare against.

    returns

    Returns true if the object is a ReadGroup, and the sampleId and id fields are equal. Else, returns false.

    Definition Classes
    ReadGroup → Equals → AnyRef → Any
  9. val flowOrder: Option[String]
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  11. def hashCode(): Int

    Generates a hash from the sampleId and id fields.

    Generates a hash from the sampleId and id fields.

    returns

    Hash code for this object.

    Definition Classes
    ReadGroup → AnyRef → Any
  12. val id: String
  13. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  14. val keySequence: Option[String]
  15. val library: Option[String]
  16. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  17. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  18. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  19. val platform: Option[String]
  20. val platformUnit: Option[String]
  21. val predictedMedianInsertSize: Option[Int]
  22. val runDateEpoch: Option[Long]
  23. val sampleId: String
  24. val sequencingCenter: Option[String]
  25. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  26. def toMetadata: formats.avro.ReadGroup

    Converts this into an Avro ReadGroup description for serialization to disk.

    Converts this into an Avro ReadGroup description for serialization to disk.

    returns

    Returns Avro version of ReadGroup.

  27. def toSAMReadGroupRecord(): SAMReadGroupRecord

    Converts a read group into a SAM formatted read group.

    Converts a read group into a SAM formatted read group.

    returns

    A SAM formatted read group.

  28. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  29. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  30. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
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    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

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