org.bdgenomics.adam.rdd.read

# AlignmentRecordDataset

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Related Docs: class AlignmentRecordDataset | package read

#### object AlignmentRecordDataset extends Serializable

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1. #### final def !=(arg0: Any): Boolean

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2. #### final def ##(): Int

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3. #### final def ==(arg0: Any): Boolean

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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.

   processingSteps

     The processing steps for the genomic dataset.

   returns

     A new AlignmentRecordDataset.

7. #### def apply(ds: Dataset[AlignmentRecord]): 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.

   returns

     A new AlignmentRecordDataset.

8. #### 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.

   processingSteps

     The processing steps for the genomic dataset.

   returns

     A new AlignmentRecordDataset.

9. #### final def asInstanceOf[T0]: T0

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10. #### def clone(): AnyRef

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13. #### def finalize(): Unit

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21. #### def toString(): String

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22. #### 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.

23. #### final def wait(): Unit

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24. #### final def wait(arg0: Long, arg1: Int): Unit

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