org.bdgenomics.adam

# models

#### package models

Visibility

1. Public
2. All

### Type Members

1. #### trait Alphabet extends AnyRef

   An alphabet of symbols and related operations

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

   A wrapper around the attrTuple (key) and value pair seen in many formats.

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. #### case class MdTag (start: Long, matches: List[NumericRange[Long]], mismatches: Map[Long, Char], deletions: Map[Long, Char]) extends Product with Serializable

   Represents the mismatches and deletions present in a read that has been aligned to a reference genome.

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

7. #### 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

   A record group represents a set of reads that were sequenced/processed/prepped/analyzed together.

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

   Builds a dictionary containing record groups.

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

10. #### class ReferencePosition extends ReferenceRegion

    A single genomic locus.

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

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

    Represents a contiguous region of the reference genome.

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

14. #### class SequenceDictionary extends Serializable

    A SequenceDictionary contains metadata about the reference build genomic data is aligned against.

15. #### 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

    Metadata about a single reference contig.

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

    A table containing all of the SNPs in a known variation dataset.

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

    A symbol in an alphabet.

18. #### class VariantContext extends Serializable

    A representation of all variation data at a single variant.

19. #### class VariantContextSerializer extends Serializer[VariantContext]

### Value Members

1. #### object Alphabet

   Singleton object with references to all supported alphabets.

2. #### object MdTag extends Serializable

   Companion object to MdTag case class.

3. #### object MdTagEvent extends Enumeration

   Enumeration describing sequence events in an MD tag:

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

   A sort order that orders all given positions lexicographically by contig and numerically within a single contig, and puts all non-provided positions at the end.

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

   A sort order that orders all given regions lexicographically by contig and numerically within a single contig, and puts all non-provided regions at the end.

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

   A sort order that orders all positions lexicographically by contig and numerically within a single contig.

7. #### object RecordGroup extends Serializable

   Singleton object for creating RecordGroups.

8. #### object RecordGroupDictionary extends Serializable

   Singleton object for creating dictionaries of record groups.

9. #### object ReferencePosition extends Serializable

   Companion object for creating and sorting ReferencePositions.

10. #### object ReferenceRegion extends Serializable

    A companion object for creating and ordering ReferenceRegions.

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

    A sort order that orders all given regions lexicographically by contig and numerically within a single contig, and puts all non-provided regions at the end.

12. #### object SequenceDictionary extends Serializable

    Singleton object for creating SequenceDictionaries.

13. #### object SequenceRecord extends Serializable

    Companion object for creating Sequence Records.

14. #### object SnpTable extends Serializable

    Companion object with helper functions for building SNP tables.

15. #### object TagType extends Enumeration

    An enumeration that describes the different data types that can be stored in an attribute.

16. #### object VariantContext extends Serializable

    Singleton object for building VariantContexts.

### Ungrouped