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.

  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.

  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