Packages

package feature

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Visibility
  1. Public
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Type Members

  1. case class BEDInFormatter extends InFormatter[Feature, Feature, FeatureDataset, BEDInFormatter] with Product with Serializable
  2. case class BEDOutFormatter(stringency: ValidationStringency = ValidationStringency.STRICT) extends OutFormatter[Feature] with Product with Serializable

    OutFormatter that reads streaming BED format.

    OutFormatter that reads streaming BED format.

    stringency

    Validation stringency. Defaults to ValidationStringency.STRICT.

  3. abstract class CoverageDataset extends MultisampleGenomicDataset[Coverage, Coverage, CoverageDataset] with GenomicDataset[Coverage, Coverage, CoverageDataset]
  4. case class DatasetBoundCoverageDataset extends CoverageDataset with DatasetBoundGenomicDataset[Coverage, Coverage, CoverageDataset] with Product with Serializable
  5. case class DatasetBoundFeatureDataset extends FeatureDataset with DatasetBoundGenomicDataset[Feature, Feature, FeatureDataset] with Product with Serializable
  6. sealed abstract class FeatureDataset extends AvroGenomicDataset[Feature, Feature, FeatureDataset] with MultisampleGenomicDataset[Feature, Feature, FeatureDataset]
  7. case class GFF3InFormatter extends InFormatter[Feature, Feature, FeatureDataset, GFF3InFormatter] with Product with Serializable
  8. case class GFF3OutFormatter(stringency: ValidationStringency = ValidationStringency.STRICT) extends OutFormatter[Feature] with Product with Serializable

    OutFormatter that reads streaming GFF3 format.

    OutFormatter that reads streaming GFF3 format.

    stringency

    Validation stringency. Defaults to ValidationStringency.STRICT.

  9. case class GTFInFormatter extends InFormatter[Feature, Feature, FeatureDataset, GTFInFormatter] with Product with Serializable
  10. case class GTFOutFormatter(stringency: ValidationStringency = ValidationStringency.STRICT) extends OutFormatter[Feature] with Product with Serializable

    OutFormatter that reads streaming GTF format.

    OutFormatter that reads streaming GTF format.

    stringency

    Validation stringency. Defaults to ValidationStringency.STRICT.

  11. case class NarrowPeakInFormatter extends InFormatter[Feature, Feature, FeatureDataset, NarrowPeakInFormatter] with Product with Serializable
  12. case class NarrowPeakOutFormatter() extends OutFormatter[Feature] with Product with Serializable

    OutFormatter that reads streaming NarrowPeak format.

  13. case class ParquetUnboundCoverageDataset extends CoverageDataset with Product with Serializable
  14. case class ParquetUnboundFeatureDataset extends FeatureDataset with Product with Serializable
  15. case class RDDBoundCoverageDataset extends CoverageDataset with Product with Serializable
  16. case class RDDBoundFeatureDataset extends FeatureDataset with Product with Serializable

Value Members

  1. object BEDInFormatter extends InFormatterCompanion[Feature, Feature, FeatureDataset, BEDInFormatter] with Serializable

    InFormatter companion that builds a BEDInFormatter to write features in BED format to a pipe.

  2. object CoverageDataset
  3. object FeatureDataset
  4. object GFF3InFormatter extends InFormatterCompanion[Feature, Feature, FeatureDataset, GFF3InFormatter] with Serializable

    InFormatter companion that builds a GFF3InFormatter to write features in GFF3 format to a pipe.

  5. object GTFInFormatter extends InFormatterCompanion[Feature, Feature, FeatureDataset, GTFInFormatter] with Serializable

    InFormatter companion that builds a GTFInFormatter to write features in GTF format to a pipe.

  6. object NarrowPeakInFormatter extends InFormatterCompanion[Feature, Feature, FeatureDataset, NarrowPeakInFormatter] with Serializable

    InFormatter companion that builds a NarrowPeakInFormatter to write features in NarrowPeak format to a pipe.

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