ADAM_2.12: Core 0.37.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package models
  Definition Classes
    adam
- Alphabet
- Attribute
- Coverage
- DNAAlphabet
- MdTag
- MdTagEvent
- OptionalPositionOrdering
- OptionalReferenceOrdering
- OptionalRegionOrdering
- PositionOrdering
- ReadGroup
- ReadGroupDictionary
- ReferenceOrdering
- ReferencePosition
- ReferencePositionSerializer
- ReferenceRegion
- ReferenceRegionSerializer
- RegionOrdering
- SequenceDictionary
- SequenceRecord
- SnpTable
- Symbol
- TagType
- VariantContext
- VariantContextSerializer

c

org.bdgenomics.adam.models

# ReadGroup 

###
Companion object ReadGroup

#### 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.

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. ReadGroup
2. Serializable
3. Serializable
4. Product
5. Equals
6. AnyRef
7. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### 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()
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.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] )
10.  val flowOrder: Option[String]
11.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
12.  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
13.  val id: String
14.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
15.  val keySequence: Option[String]
16.  val library: Option[String]
17.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
18.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
19.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
20.  val platform: Option[String]
21.  val platformUnit: Option[String]
22.  val predictedMedianInsertSize: Option[Int]
23.  val runDateEpoch: Option[Long]
24.  val sampleId: String
25.  val sequencingCenter: Option[String]
26.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
27.  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.

28.  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.

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

### Inherited from Serializable

### Inherited from Product

### Inherited from Equals

### Inherited from AnyRef

### Inherited from Any

### Ungrouped