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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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
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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- val description: Option[String]
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final
def
eq(arg0: AnyRef): Boolean
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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
- val flowOrder: Option[String]
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final
def
getClass(): Class[_]
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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
- val id: String
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final
def
isInstanceOf[T0]: Boolean
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- val keySequence: Option[String]
- val library: Option[String]
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ne(arg0: AnyRef): Boolean
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def
notify(): Unit
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def
notifyAll(): Unit
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- val platform: Option[String]
- val platformUnit: Option[String]
- val predictedMedianInsertSize: Option[Int]
- val runDateEpoch: Option[Long]
- val sampleId: String
- val sequencingCenter: Option[String]
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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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.
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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.
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def
wait(arg0: Long, arg1: Int): Unit
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wait(arg0: Long): Unit
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wait(): Unit
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finalize(): Unit
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