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org.bdgenomics.adam.rdd.fragment

FragmentDataset

Related Docs: class FragmentDataset | package fragment

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object FragmentDataset

Helper singleton object for building FragmentDatasets.

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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_QUALITY_SCORES: String

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    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

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    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, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentDataset

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    A genomic dataset that supports Datasets of Fragments.

    A genomic dataset that supports Datasets of Fragments.

    ds

    The underlying Dataset of Fragment data.

    sequences

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

    readGroups

    The read groups these Fragments came from.

    processingSteps

    The processing steps that have been applied to this data.

    returns

    A new FragmentDataset.

  7. def apply(ds: Dataset[Fragment]): FragmentDataset

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    A genomic dataset that supports Datasets of Fragments.

    A genomic dataset that supports Datasets of Fragments.

    ds

    The underlying Dataset of Fragment data.

    returns

    A new FragmentDataset.

  8. def apply(rdd: RDD[Fragment], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentDataset

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    Builds a FragmentDataset without a partition map.

    Builds a FragmentDataset without a partition map.

    rdd

    The underlying Fragment RDD.

    sequences

    The sequence dictionary for the genomic dataset.

    readGroups

    The read group dictionary for the genomic dataset.

    processingSteps

    The processing steps that have been applied to this data.

    returns

    A new FragmentDataset.

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