ADAM_2.12: Core 0.30.0 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
- AlignmentDataset
- AnySAMInFormatter
- AnySAMInFormatterCompanion
- AnySAMOutFormatter
- BAMInFormatter
- DatasetBoundAlignmentDataset
- DatasetBoundReadDataset
- FASTQInFormatter
- IncorrectMDTagException
- InstrumentedADAMBAMOutputFormat
- InstrumentedADAMBAMOutputFormatHeaderLess
- InstrumentedADAMCRAMOutputFormat
- InstrumentedADAMCRAMOutputFormatHeaderLess
- InstrumentedADAMSAMOutputFormat
- InstrumentedADAMSAMOutputFormatHeaderLess
- ParquetUnboundAlignmentDataset
- ParquetUnboundReadDataset
- QualityScoreBin
- RDDBoundAlignmentDataset
- RDDBoundReadDataset
- ReadDataset
- ReferencePositionPairSerializer
- SAMInFormatter
- SingleReadBucketSerializer

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org.bdgenomics.adam.rdd.read

# AlignmentDataset 

###
Companion class AlignmentDataset

#### object AlignmentDataset extends Serializable

Linear Supertypes
Serializable, Serializable, AnyRef, Any
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### 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.  val WRITE_ORIGINAL_QUALITY_SCORES: String

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

   Hadoop configuration path to check for a boolean value indicating whether the current or original read quality scores should be written. True indicates to write the original quality scores. 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[Alignment], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentDataset

   Builds an AlignmentDataset without a partition map from a Dataset.

   Builds an AlignmentDataset without a partition map from a Dataset.

   ds

     The underlying Alignment Dataset.

   sequences

     The sequence dictionary for the genomic dataset.

   readGroups

     The read group dictionary for the genomic dataset.

   processingSteps

     The processing steps for the genomic dataset.

   returns

     A new AlignmentDataset.

7.  def apply(ds: Dataset[Alignment]): AlignmentDataset

   Builds an AlignmentDataset without a partition map from a Dataset.

   Builds an AlignmentDataset without a partition map from a Dataset.

   ds

     The underlying Alignment Dataset.

   returns

     A new AlignmentDataset.

8.  def apply(rdd: RDD[Alignment], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentDataset

   Builds an AlignmentDataset without a partition map from an RDD.

   Builds an AlignmentDataset without a partition map from an RDD.

   rdd

     The underlying Alignment RDD.

   sequences

     The sequence dictionary for the genomic dataset.

   readGroups

     The read group dictionary for the genomic dataset.

   processingSteps

     The processing steps for the genomic dataset.

   returns

     A new AlignmentDataset.

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

    Builds an AlignmentDataset for unaligned reads.

    Builds an AlignmentDataset for unaligned reads.

    rdd

      The underlying Alignment RDD.

    returns

      A new AlignmentDataset.

23.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
24.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
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      @throws( ... )
25.  final def wait(arg0: Long): Unit
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      @native() @throws( ... )

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

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