org.bdgenomics.adam

models

package models

Visibility
  1. Public
  2. All

Type Members

  1. case class Attribute(tag: String, tagType: TagType.Value, value: Any) extends Product with Serializable

    A wrapper around the attrTuple (key) and value pair.

  2. class BEDFeature extends BaseFeature

  3. class BaseFeature extends AnyRef

  4. case class Consensus(consensus: String, index: ReferenceRegion) extends Product with Serializable

  5. class IndelTable extends Serializable with Logging

  6. trait Interval extends AnyRef

    An interval is a region on a coordinate space that has a defined width.

  7. class NarrowPeakFeature extends BaseFeature

  8. class OrderedTrackedLayout[T] extends TrackedLayout[T]

    An implementation of TrackedLayout which takes a sequence of ReferenceMappable values, and lays them out in order (i.

  9. case class ProgramRecord(id: String, commandLine: Option[String], name: Option[String], version: Option[String], previousID: Option[String]) extends Product with Serializable

  10. case class ReadBucket(unpairedPrimaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedFirstPrimaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedSecondPrimaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], unpairedSecondaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedFirstSecondaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedSecondSecondaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], unmappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing]) extends Product with Serializable

    This class is similar to SingleReadBucket, except it breaks the reads down further.

  11. class ReadBucketSerializer extends Serializer[ReadBucket]

  12. class RecordGroup extends Serializable

  13. class RecordGroupDictionary extends Serializable

    Builds a dictionary containing record groups.

  14. trait ReferenceMapping[T] extends AnyRef

  15. case class ReferencePosition(referenceName: String, pos: Long) extends Ordered[ReferencePosition] with Product with Serializable

  16. case class ReferencePositionPair(read1refPos: Option[ReferencePositionWithOrientation], read2refPos: Option[ReferencePositionWithOrientation]) extends Product with Serializable

  17. class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

  18. class ReferencePositionSerializer extends Serializer[ReferencePosition]

  19. case class ReferencePositionWithOrientation(refPos: Option[ReferencePosition], negativeStrand: Boolean) extends Ordered[ReferencePositionWithOrientation] with Product with Serializable

  20. class ReferencePositionWithOrientationSerializer extends Serializer[ReferencePositionWithOrientation]

  21. case class ReferenceRegion(referenceName: String, start: Long, end: Long) extends Ordered[ReferenceRegion] with Interval with Product with Serializable

    Represents a contiguous region of the reference genome.

  22. class ReferenceRegionSerializer extends Serializer[ReferenceRegion]

  23. case class ReferenceRegionWithOrientation(referenceName: String, start: Long, end: Long, negativeStrand: Boolean) extends Ordered[ReferenceRegionWithOrientation] with Product with Serializable

    Represents a contiguous region of the reference genome with strand information.

  24. case class Rod(position: ReferencePosition, pileups: List[Pileup]) extends Product with Serializable

    Class representing a set of pileup bases at a specific locus.

  25. class SAMFileHeaderWritable extends Serializable

  26. class SequenceDictionary extends Serializable

  27. class SequenceRecord extends Serializable

    Utility class within the SequenceDictionary; represents unique reference name-to-id correspondence

  28. case class SingleReadBucket(primaryMapped: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], secondaryMapped: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], unmapped: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing]) extends Product with Serializable

  29. class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

  30. class SnpTable extends Serializable with Logging

  31. trait TrackedLayout[T] extends AnyRef

    A TrackedLayout is an assignment of values of some type T (which presumably are mappable to a reference genome or other linear coordinate space) to 'tracks' -- that is, to integers, with the guarantee that no two values assigned to the same track will overlap.

  32. case class VCFHeaderWritable(header: VCFHeader) extends Product with Serializable

  33. class VariantContext extends AnyRef

Value Members

  1. object Consensus extends Serializable

  2. object IndelTable extends Serializable

  3. object ProgramRecord extends Serializable

  4. object ReadBucket extends Serializable

  5. object RecordGroup extends Serializable

  6. object RecordGroupDictionary extends Serializable

  7. object ReferencePosition extends Serializable

  8. object ReferencePositionPair extends Logging with Serializable

  9. object ReferencePositionWithOrientation extends Serializable

  10. object ReferenceRegion extends Serializable

  11. object ReferenceRegionWithOrientation extends Serializable

  12. object SAMFileHeaderWritable extends Serializable

  13. object SequenceDictionary extends Serializable

    SequenceDictionary contains the (bijective) map between Ints (the referenceId) and Strings (the referenceName) from the header of a BAM file, or the combined result of multiple such SequenceDictionaries.

  14. object SequenceRecord extends Serializable

  15. object SingleReadBucket extends Logging with Serializable

  16. object SnpTable extends Serializable

  17. object TagType extends Enumeration

  18. object TrackedLayout

  19. object VariantContext

    Note: VariantContext inherits its name from the Picard VariantContext, and is not related to the SparkContext object.

Ungrouped