org.bdgenomics.adam.rdd

# feature

#### package feature

Visibility

1. Public
2. All

### 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.

### Ungrouped