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