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. 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. 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.

  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] = 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.

  10. class ReadBucketSerializer extends Serializer[ReadBucket]

  11. 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

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

    Builds a dictionary containing record groups.

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

    Represents a contiguous region of the reference genome.

  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] = 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

  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

  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.

Ungrouped