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. class BEDFeature extends BaseFeature

  4. class BaseFeature extends Serializable

  5. abstract class BlockExtractable extends Extractable

  6. case class CDS(transcriptId: String, strand: Boolean, region: ReferenceRegion) extends BlockExtractable with Product with Serializable

    Coding Sequence annotations, should be a subset of an Exon for a particular Transcript

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

  8. class DNAAlphabet extends Alphabet

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

  9. case class Exon(exonId: String, transcriptId: String, strand: Boolean, region: ReferenceRegion) extends BlockExtractable with Product with Serializable

    An exon model (here represented as a value of the Exon class) is a representation of a single exon from a transcript in genomic coordinates.

  10. trait Extractable extends AnyRef

    A trait for values (usually regions or collections of regions) that can be subsetted or extracted out of a larger region string -- for example, exons or transcripts which have a sequence defined in terms of their coordinates against a reference chromosome.

  11. class GTFFeature extends BaseFeature

  12. case class Gene(id: String, names: Seq[String], strand: Boolean, transcripts: Iterable[Transcript]) extends Product with Serializable

    A 'gene model' is a small, hierarchical collection of objects: Genes, Transcripts, and Exons.

  13. class IndelTable extends Serializable with Logging

  14. trait Interval extends AnyRef

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

  15. class NarrowPeakFeature extends BaseFeature

    See: http://genome.

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

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

  18. 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.

  19. class ReadBucketSerializer extends Serializer[ReadBucket]

  20. class RecordGroup extends Serializable

  21. class RecordGroupDictionary extends Serializable

    Builds a dictionary containing record groups.

  22. trait ReferenceOrdering[T <: ReferenceRegion] extends Ordering[T]

  23. class ReferencePosition extends ReferenceRegion

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

  25. class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

  26. class ReferencePositionSerializer extends Serializer[ReferencePosition]

  27. 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.

  28. class ReferenceRegionSerializer extends Serializer[ReferenceRegion]

  29. class SAMFileHeaderWritable extends Serializable

  30. class SequenceDictionary extends Serializable

  31. class SequenceRecord extends Serializable

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

  32. 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

  33. class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

  34. class SnpTable extends Serializable with Logging

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

    A symbol in an alphabet

  36. case class Transcript(id: String, names: Seq[String], geneId: String, strand: Boolean, exons: Iterable[Exon], cds: Iterable[CDS], utrs: Iterable[UTR]) extends Product with Serializable

    A transcript model (here represented as a value of the Transcript class) is a simple, hierarchical model containing a collection of exon models as well as an associated gene identifier, transcript identifier, and a set of common names (synonyms).

  37. case class UTR(transcriptId: String, strand: Boolean, region: ReferenceRegion) extends BlockExtractable with Product with Serializable

    UnTranslated Regions

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

  39. class VariantContext extends AnyRef

Value Members

  1. object Alphabet

  2. object BEDFeature extends Serializable

  3. object BaseFeature extends Serializable

  4. object Consensus extends Serializable

  5. object IndelTable extends Serializable

  6. object OptionalPositionOrdering extends OptionalReferenceOrdering[ReferencePosition]

  7. object OptionalRegionOrdering extends OptionalReferenceOrdering[ReferenceRegion]

  8. object PositionOrdering extends ReferenceOrdering[ReferencePosition]

  9. object ProgramRecord extends Serializable

  10. object ReadBucket extends Serializable

  11. object RecordGroup extends Serializable

  12. object RecordGroupDictionary extends Serializable

  13. object ReferencePosition extends Serializable

  14. object ReferencePositionPair extends Logging with Serializable

  15. object ReferenceRegion extends Serializable

  16. object ReferenceUtils

  17. object RegionOrdering extends ReferenceOrdering[ReferenceRegion]

  18. object SAMFileHeaderWritable extends Serializable

  19. 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.

  20. object SequenceRecord extends Serializable

  21. object SingleReadBucket extends Logging with Serializable

  22. object SnpTable extends Serializable

  23. object TagType extends Enumeration

  24. object VariantContext

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

Ungrouped