object AlignmentDataset extends Serializable

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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.

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  20. def toString(): String
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  21. 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.

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