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.

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

   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.

   This class is roughly analogous to htsjdk's 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(referenceName: String, start: Long, end: Long, count: Double, optSampleId: Option[String] = None) extends Product with Serializable

   Coverage record for CoverageDataset.

   Coverage record for CoverageDataset.

   Contains Region indexed by reference name, start and end, as well as the average coverage at each base pair in that region.

   referenceName

     The chromosome that this coverage was observed on.

   start

     The start coordinate of the region where this coverage value was observed.

   end

     The end coordinate of the region where this coverage value was observed.

   count

     The average coverage across this region.

   optSampleId

     Option of sampleId for this Coverage record

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.

   Represents the mismatches and deletions present in a read that has been aligned to a reference genome. The MD tag can be used to reconstruct the reference that an aligned read overlaps.

   start

     Start position of the alignment.

   matches

     A list of the ranges over which the read has a perfect sequence match.

   mismatches

     A map of all the locations where a base mismatched.

   deletions

     A map of all locations where a base was deleted.

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

7. #### case class ReadGroup(sampleId: String, id: 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

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

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

   sampleId

     The sample these reads are from.

   id

     The identifier for this read group.

   sequencingCenter

     The optional name of the place where these reads were sequenced.

   description

     An optional description for this read group.

   runDateEpoch

     An optional Unix epoch timestamp for when these reads were run through the sequencer.

   flowOrder

     An optional string of nucleotides that were used for each flow of each read.

   keySequence

     An optional string of nucleotides that are the key for this read.

   library

     An optional library name.

   predictedMedianInsertSize

     An optional prediction of the read insert size for this library prep.

   platform

     An optional description for the platform this group was sequenced on.

   platformUnit

     An optional ID for the sequencer this group was sequenced on.

8. #### case class ReadGroupDictionary(readGroups: Seq[ReadGroup]) extends Product with Serializable

   Builds a dictionary containing read groups.

   Builds a dictionary containing read groups.

   Read 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.

   readGroups

     A seq of read groups to populate the dictionary.

   Exceptions thrown

     `IllegalArgumentException` Throws an assertion error if there are multiple read groups with the same name.

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

    strand

      The strand of the genome that this region exists on.

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

14. #### class SequenceDictionary extends Serializable

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

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

    See also

      SequenceRecord

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], index: Option[Int]) extends Serializable with Product

    Metadata about a single reference sequence.

    Metadata about a single reference sequence.

    name

      The name of this reference in the assembly.

    length

      The length of the sequence for this reference.

    url

      If available, the URI from which the reference sequence was obtained.

    md5

      If available, the MD5 checksum uniquely representing this reference as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (equivalent to SQ:M5 in SAM).

    refseq

      If available, the REFSEQ ID for the reference.

    genbank

      If available, the Genbank ID for the reference.

    assembly

      If available, the name of the assembly for this reference.

    species

      If available, the species that this reference is for.

    index

      If available, the number of this reference in a set of references.

16. #### class SnpTable extends Serializable

    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.

    A symbol in an alphabet.

    label

      a character which represents the symbol

    complement

      acharacter which represents the complement of the symbol

18. #### class VariantContext extends Serializable

    A representation of all variation data at a single variant.

    A representation of all variation data at a single variant.

    This class represents an equivalent to a single allele from a VCF line, and is the ADAM equivalent to htsjdk.variant.variantcontext.VariantContext.

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.

   Companion object to MdTag case class. Provides methods for building an MdTag model from a read.

3. #### object MdTagEvent extends Enumeration

   Enumeration describing sequence events in an MD tag:

   Enumeration describing sequence events in an MD tag:

   * Match is a sequence match (i.e., every base in the aligned sequence matches the reference sequence) * Mismatch is a sequence mismatch (there are bases that do not match the reference sequence) * Delete indicates that bases that were present in the reference sequence were deleted in the read sequence

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

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

   A sort order that orders all given positions lexicographically by reference and numerically within a single reference, and puts all non-provided positions at the end. An extension of PositionOrdering to Optional data.

   See also

     PositionOrdering

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

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

   A sort order that orders all given regions lexicographically by reference and numerically within a single reference sequence, and puts all non-provided regions at the end. An extension of PositionOrdering to Optional data.

   See also

     PositionOrdering

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

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

7. #### object ReadGroup extends Serializable

   Singleton object for creating ReaGroups.

8. #### object ReadGroupDictionary extends Serializable

   Singleton object for creating dictionaries of read 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 reference and numerically within a single reference sequence, and puts all non-provided regions at the end.

    A sort order that orders all given regions lexicographically by reference and numerically within a single reference sequence, and puts all non-provided regions at the end. Regions are compared by start position first. If start positions are equal, then we compare by end position.

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