org.bdgenomics.adam.rdd

# feature

#### package feature

Visibility

1. Public
2. All

### Type Members

1. #### case class BEDInFormatter extends InFormatter[Feature, Feature, FeatureRDD, 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 CoverageRDD extends MultisampleGenomicDataset[Coverage, Coverage, CoverageRDD] with GenomicDataset[Coverage, Coverage, CoverageRDD]

4. #### case class DatasetBoundCoverageRDD extends CoverageRDD with DatasetBoundGenomicDataset[Coverage, Coverage, CoverageRDD] with Product with Serializable

   A Dataset containing Coverage data.

5. #### case class DatasetBoundFeatureRDD extends FeatureRDD with DatasetBoundGenomicDataset[Feature, Feature, FeatureRDD] with Product with Serializable

6. #### sealed abstract class FeatureRDD extends AvroGenomicDataset[Feature, Feature, FeatureRDD] with MultisampleGenomicDataset[Feature, Feature, FeatureRDD]

7. #### case class GFF3InFormatter extends InFormatter[Feature, Feature, FeatureRDD, 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, FeatureRDD, 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, FeatureRDD, 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 ParquetUnboundCoverageRDD extends CoverageRDD with Product with Serializable

14. #### case class ParquetUnboundFeatureRDD extends FeatureRDD with Product with Serializable

15. #### case class RDDBoundCoverageRDD extends CoverageRDD with Product with Serializable

    An RDD containing Coverage data.

16. #### case class RDDBoundFeatureRDD extends FeatureRDD with Product with Serializable

### Value Members

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

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

2. #### object CoverageRDD

3. #### object FeatureRDD

4. #### object GFF3InFormatter extends InFormatterCompanion[Feature, Feature, FeatureRDD, 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, FeatureRDD, 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, FeatureRDD, NarrowPeakInFormatter] with Serializable

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

### Ungrouped