ADAM_2.12: Core 0.27.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package rdd
  Definition Classes
    adam
-  package read
  Definition Classes
    rdd
- ADAMBAMOutputFormat
- ADAMBAMOutputFormatHeaderLess
- ADAMCRAMOutputFormat
- ADAMCRAMOutputFormatHeaderLess
- ADAMSAMOutputFormat
- ADAMSAMOutputFormatHeaderLess
- AlignmentRecordDataset
- AnySAMInFormatter
- AnySAMInFormatterCompanion
- AnySAMOutFormatter
- BAMInFormatter
- DatasetBoundAlignmentRecordDataset
- FASTQInFormatter
- IncorrectMDTagException
- InstrumentedADAMBAMOutputFormat
- InstrumentedADAMBAMOutputFormatHeaderLess
- InstrumentedADAMCRAMOutputFormat
- InstrumentedADAMCRAMOutputFormatHeaderLess
- InstrumentedADAMSAMOutputFormat
- InstrumentedADAMSAMOutputFormatHeaderLess
- ParquetUnboundAlignmentRecordDataset
- QualityScoreBin
- RDDBoundAlignmentRecordDataset
- ReferencePositionPairSerializer
- SAMInFormatter
- SingleReadBucketSerializer

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org.bdgenomics.adam.rdd.read

# AlignmentRecordDataset 

###
Companion class AlignmentRecordDataset

#### object AlignmentRecordDataset extends Serializable

Linear Supertypes
Serializable, Serializable, AnyRef, Any
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### Value Members

1.  final def !=(arg0: Any): Boolean
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     AnyRef → Any
2.  final def ##(): Int
   Definition Classes
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
4.  val WRITE_ORIGINAL_QUALITIES: String

   Hadoop configuration path to check for a boolean value indicating whether the current or original read qualities should be written.

   Hadoop configuration path to check for a boolean value indicating whether the current or original read qualities should be written. True indicates to write the original qualities. The default is false.

5.  val WRITE_SUFFIXES: String

   Hadoop configuration path to check for a boolean value indicating whether to write the "/1" "/2" suffixes to the read name that indicate whether a read is first or second in a pair.

   Hadoop configuration path to check for a boolean value indicating whether to write the "/1" "/2" suffixes to the read name that indicate whether a read is first or second in a pair. Default is false (no suffixes).

6.  def apply(ds: Dataset[AlignmentRecord], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentRecordDataset

   Builds an AlignmentRecordDataset without a partition map from a Dataset.

   Builds an AlignmentRecordDataset without a partition map from a Dataset.

   ds

     The underlying AlignmentRecord Dataset.

   sequences

     The sequence dictionary for the genomic dataset.

   readGroups

     The read group dictionary for the genomic dataset.

   returns

     A new AlignmentRecordDataset.

7.  def apply(rdd: RDD[AlignmentRecord], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentRecordDataset

   Builds an AlignmentRecordDataset without a partition map from an RDD.

   Builds an AlignmentRecordDataset without a partition map from an RDD.

   rdd

     The underlying AlignmentRecord RDD.

   sequences

     The sequence dictionary for the genomic dataset.

   readGroups

     The read group dictionary for the genomic dataset.

   returns

     A new AlignmentRecordDataset.

8.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
9.  def clone(): AnyRef
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     protected[java.lang]
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     @native() @throws( ... )
10.  final def eq(arg0: AnyRef): Boolean
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11.  def equals(arg0: Any): Boolean
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12.  def finalize(): Unit
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13.  final def getClass(): Class[_]
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14.  def hashCode(): Int
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15.  final def isInstanceOf[T0]: Boolean
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16.  final def ne(arg0: AnyRef): Boolean
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17.  final def notify(): Unit
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18.  final def notifyAll(): Unit
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19.  final def synchronized[T0](arg0: ⇒ T0): T0
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20.  def toString(): String
    Definition Classes
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21.  def unaligned(rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

    Builds an AlignmentRecordDataset for unaligned reads.

    Builds an AlignmentRecordDataset for unaligned reads.

    rdd

      The underlying AlignmentRecord RDD.

    returns

      A new AlignmentRecordDataset.

22.  final def wait(): Unit
    Definition Classes
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      @throws( ... )
23.  final def wait(arg0: Long, arg1: Int): Unit
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24.  final def wait(arg0: Long): Unit
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### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

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