org.bdgenomics.adam.rdd

# feature

#### package feature

Visibility

1. Public
2. All

### Type Members

1. #### case class BEDInFormatter extends InFormatter[Feature, FeatureRDD, BEDInFormatter] with Product with Serializable

2. #### case class BEDOutFormatter () extends OutFormatter[Feature] with Product with Serializable

   OutFormatter that reads streaming BED format.

3. #### case class CoverageRDD (rdd: RDD[Coverage], sequences: SequenceDictionary) extends GenomicRDD[Coverage, CoverageRDD] with Product with Serializable

   An RDD containing Coverage data.

   An RDD containing Coverage data.

   rdd

     An RDD containing data describing how many reads cover a genomic locus/region.

   sequences

     A dictionary describing the reference genome.

4. #### case class FeatureRDD (rdd: RDD[Feature], sequences: SequenceDictionary) extends AvroGenomicRDD[Feature, FeatureRDD] with Logging with Product with Serializable

   A GenomicRDD that wraps Feature data.

   A GenomicRDD that wraps Feature data.

   rdd

     An RDD of genomic Features.

   sequences

     The reference genome this data is aligned to.

5. #### case class GFF3InFormatter extends InFormatter[Feature, FeatureRDD, GFF3InFormatter] with Product with Serializable

6. #### case class GFF3OutFormatter () extends OutFormatter[Feature] with Product with Serializable

   OutFormatter that reads streaming GFF3 format.

7. #### case class GTFInFormatter extends InFormatter[Feature, FeatureRDD, GTFInFormatter] with Product with Serializable

8. #### case class GTFOutFormatter () extends OutFormatter[Feature] with Product with Serializable

   OutFormatter that reads streaming GTF format.

9. #### case class NarrowPeakInFormatter extends InFormatter[Feature, FeatureRDD, NarrowPeakInFormatter] with Product with Serializable

10. #### case class NarrowPeakOutFormatter () extends OutFormatter[Feature] with Product with Serializable

    OutFormatter that reads streaming NarrowPeak format.

### Value Members

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

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

2. #### object FeatureRDD extends Serializable

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

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

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

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

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

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

### Ungrouped