FragmentRDD

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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[Fragment], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentRDD

   

   A genomic RDD that supports Datasets of Fragments.

   A genomic RDD that supports Datasets of Fragments.

   ds

   The underlying Dataset of Fragment data.

   sequences

   The genomic sequences this data was aligned to, if any.

   recordGroups

   The record groups these Fragments came from.

   processingSteps

   The processing steps that have been applied to this data.

   returns

   A new FragmentRDD.

7. def apply(rdd: RDD[Fragment], sequences: SequenceDictionary, recordGroupDictionary: RecordGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentRDD

   

   Builds a FragmentRDD without a partition map.

   Builds a FragmentRDD without a partition map.

   rdd

   The underlying Franment RDD.

   sequences

   The sequence dictionary for the RDD.

   recordGroupDictionary

   The record group dictionary for the RDD.

   processingSteps

   The processing steps that have been applied to this data.

   returns

   A new FragmentRDD.

8. final def asInstanceOf[T0]: T0

   

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9. def clone(): AnyRef

   

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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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21. final def wait(): Unit

    

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

    

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23. final def wait(arg0: Long): Unit

    

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