org.bdgenomics.adam.rdd.read

# AlignmentRecordRDD

#### object AlignmentRecordRDD extends Serializable

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

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

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

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4. #### final def ==(arg0: AnyRef): Boolean

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

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6. #### 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.

7. #### 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).

8. #### def apply(ds: Dataset[AlignmentRecord], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentRecordRDD

9. #### def apply(rdd: RDD[AlignmentRecord], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentRecordRDD

   Builds an AlignmentRecordRDD without a partition map.

   Builds an AlignmentRecordRDD without a partition map.

   rdd

     The underlying AlignmentRecord RDD.

   sequences

     The sequence dictionary for the RDD.

   recordGroups

     The record group dictionary for the RDD.

   returns

     A new AlignmentRecordRDD.

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

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

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12. #### final def eq(arg0: AnyRef): Boolean

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

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15. #### final def getClass(): Class[_]

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16. #### def hashCode(): Int

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17. #### final def isInstanceOf[T0]: Boolean

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18. #### final def ne(arg0: AnyRef): Boolean

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

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

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21. #### final def synchronized[T0](arg0: ⇒ T0): T0

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

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23. #### def unaligned(rdd: RDD[AlignmentRecord]): AlignmentRecordRDD

    Builds an AlignmentRecordRDD for unaligned reads.

    Builds an AlignmentRecordRDD for unaligned reads.

    rdd

      The underlying AlignmentRecord RDD.

    returns

      A new AlignmentRecordRDD.

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

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

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26. #### final def wait(arg0: Long): Unit

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