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.

   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

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

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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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17. #### final def notify(): Unit

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18. #### final def notifyAll(): Unit

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

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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

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

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