AlignmentDataset

Value Members

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_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

   

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10. def clone(): AnyRef

    

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    protected[java.lang]

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11. final def eq(arg0: AnyRef): Boolean

    

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12. def equals(arg0: Any): Boolean

    

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13. def finalize(): Unit

    

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14. final def getClass(): Class[_]

    

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15. def hashCode(): Int

    

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16. final def isInstanceOf[T0]: Boolean

    

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17. final def ne(arg0: AnyRef): Boolean

    

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18. final def notify(): Unit

    

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19. final def notifyAll(): Unit

    

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

    

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21. def toString(): String

    

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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

    

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

    

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

    

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