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.

   Created by bryan on 4/17/15.

   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.

   A wrapper around the attrTuple (key) and value pair. Includes the attrTuple-type explicitly, rather than embedding the corresponding information in the type of 'value', because otherwise it'd be difficult to extract the correct type for Byte and NumericSequence values.

   Roughly analogous to Picards SAMTagAndValue.

   tag

     The string key associated with this pair.

   tagType

     An enumerated value representing the type of the 'value' parameter.

   value

     The 'value' half of the pair.

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

   Coverage record for CoverageRDD.

   Coverage record for CoverageRDD. Contains Region indexed by contig name, start and end, as well as count of coverage at each base pair in that region.

   contigName

     Specifies chromosomal location of coverage

   start

     Specifies start position of coverage

   end

     Specifies end position of coverage

   count

     Specifies count of coverage at location

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.

   The evaluation of a regionJoin takes place with respect to a complete partition on the total space of the genome. NonoverlappingRegions is a class to compute the value of that partition, and to allow us to assign one or more elements of that partition to a new ReferenceRegion (see the 'regionsFor' method).

   NonoverlappingRegions takes, as input, and 'input-set' of regions. These are arbitrary ReferenceRegions, which may be overlapping, identical, disjoint, etc. The input-set of regions _must_ all be located on the same reference chromosome (i.e. must all have the same refName); the generalization to reference regions from multiple chromosomes is in MultiContigNonoverlappingRegions, below.

   NonoverlappingRegions produces, internally, a 'nonoverlapping-set' of regions. This is basically the set of _distinct unions_ of the input-set regions.

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] = Seq.empty, pairedFirstPrimaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedSecondPrimaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, unpairedSecondaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedFirstSecondaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedSecondSecondaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, unmappedReads: Iterable[AlignmentRecord] = Seq.empty) extends Product with Serializable

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

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

   Rather than stopping at primary/secondary/unmapped, this will break it down further into whether they are paired or unpaired, and then whether they are the first or second of the pair.

   This is useful as this will usually map a single read in any of the sequences.

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

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

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

    Builds a dictionary containing record groups.

    Builds a dictionary containing record groups. Record groups must have a unique name across all samples in the dictionary. This dictionary provides numerical IDs for each group; these IDs are only consistent when referencing a single dictionary.

    recordGroups

      A seq of record groups to popualate the dictionary.

    Exceptions thrown

      `AssertionError` Throws an assertion error if there are multiple record groups with the same name.

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 = Strand.INDEPENDENT) extends Comparable[ReferenceRegion] with Interval with Product with Serializable

    Represents a contiguous region of the reference genome.

    Represents a contiguous region of the reference genome.

    referenceName

      The name of the sequence (chromosome) in the reference genome

    start

      The 0-based residue-coordinate for the start of the region

    end

      The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e. [start, end) define a 0-based half-open interval.

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] = Seq.empty, secondaryMapped: Iterable[AlignmentRecord] = Seq.empty, unmapped: Iterable[AlignmentRecord] = Seq.empty) 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

    A symbol in an alphabet

    label

      a character which represents the symbol

    complement

      acharacter which represents the complement of the symbol

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.

    Note: VariantContext inherits its name from the Picard VariantContext, and is not related to the SparkContext object. If you're looking for the latter, see org.bdgenomics.adam.rdd.variation.VariationContext

### Ungrouped