object AlignmentRecordDataset extends Serializable

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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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  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.

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