org.bdgenomics.adam

# models

#### package models

Visibility

1. Public
2. All

### Type Members

1. #### trait Alphabet extends AnyRef

   Created by bryan on 4/17/15.

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

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

3. #### case class Coverage(contigName: String, start: Long, end: Long, count: Double) extends Product with Serializable

   Coverage record for CoverageRDD.

4. #### class DNAAlphabet extends Alphabet

   The standard DNA alphabet with A,T,C, and G

5. #### class MultiContigNonoverlappingRegions extends Serializable

   Creates a multi-reference-region collection of NonoverlappingRegions -- see the scaladocs to NonoverlappingRegions.

6. #### class NonoverlappingRegions extends Serializable

   The evaluation of a regionJoin takes place with respect to a complete partition on the total space of the genome.

7. #### trait OptionalReferenceOrdering[T <: ReferenceRegion] extends Ordering[Option[T]]

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

9. #### 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.

10. #### class ReadBucketSerializer extends Serializer[ReadBucket]

11. #### case class RecordGroup(sample: String, recordGroupName: String, sequencingCenter: Option[String] = scala.None, description: Option[String] = scala.None, runDateEpoch: Option[Long] = scala.None, flowOrder: Option[String] = scala.None, keySequence: Option[String] = scala.None, library: Option[String] = scala.None, predictedMedianInsertSize: Option[Int] = scala.None, platform: Option[String] = scala.None, platformUnit: Option[String] = scala.None) extends Product with Serializable

12. #### case class RecordGroupDictionary(recordGroups: Seq[RecordGroup]) extends Product with Serializable

    Builds a dictionary containing record groups.

13. #### trait ReferenceOrdering[T <: ReferenceRegion] extends Ordering[T]

14. #### class ReferencePosition extends ReferenceRegion

15. #### case class ReferencePositionPair(read1refPos: Option[ReferencePosition], read2refPos: Option[ReferencePosition]) extends Product with Serializable

16. #### class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

17. #### class ReferencePositionSerializer extends Serializer[ReferencePosition]

18. #### case class ReferenceRegion(referenceName: String, start: Long, end: Long, orientation: Strand = ...) extends Comparable[ReferenceRegion] with Interval with Product with Serializable

    Represents a contiguous region of the reference genome.

19. #### class ReferenceRegionSerializer extends Serializer[ReferenceRegion]

20. #### class SAMFileHeaderWritable extends Serializable

21. #### class SequenceDictionary extends Serializable

22. #### case class SequenceRecord(name: String, length: Long, url: Option[String], md5: Option[String], refseq: Option[String], genbank: Option[String], assembly: Option[String], species: Option[String], referenceIndex: Option[Int]) extends Serializable with Product

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

23. #### 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

24. #### class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

25. #### class SnpTable extends Serializable with Logging

26. #### case class Symbol(label: Char, complement: Char) extends Product with Serializable

    A symbol in an alphabet

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

28. #### class VariantContext extends AnyRef

### Value Members

1. #### object Alphabet

2. #### object Coverage extends Serializable

   Converts from avro Feature to Coverage.

3. #### object MultiContigNonoverlappingRegions extends Serializable

4. #### object NonoverlappingRegions extends Serializable

5. #### object OptionalPositionOrdering extends OptionalReferenceOrdering[ReferencePosition]

6. #### object OptionalRegionOrdering extends OptionalReferenceOrdering[ReferenceRegion]

7. #### object PositionOrdering extends ReferenceOrdering[ReferencePosition]

8. #### object ProgramRecord extends Serializable

9. #### object ReadBucket extends Serializable

10. #### object RecordGroup extends Serializable

11. #### object RecordGroupDictionary extends Serializable

12. #### object ReferencePosition extends Serializable

13. #### object ReferencePositionPair extends Logging with Serializable

14. #### object ReferenceRegion extends Serializable

15. #### object RegionOrdering extends ReferenceOrdering[ReferenceRegion]

16. #### 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.

17. #### object SequenceOrderingByName extends Ordering[SequenceRecord]

18. #### object SequenceOrderingByRefIdx extends Ordering[SequenceRecord]

19. #### object SequenceRecord extends Serializable

20. #### object SingleReadBucket extends Logging with Serializable

21. #### object SnpTable extends Serializable

22. #### object TagType extends Enumeration

23. #### object VariantContext

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

### Ungrouped