Package

org.bdgenomics.adam

models

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package models

Visibility
  1. Public
  2. All

Type Members

  1. trait Alphabet extends AnyRef

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    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

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    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

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    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

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

  5. class MultiContigNonoverlappingRegions extends Serializable

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    Creates a multi-reference-region collection of NonoverlappingRegions -- see the scaladocs to NonoverlappingRegions.

  6. class NonoverlappingRegions extends Serializable

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    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]]

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

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  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

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    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]

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  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

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

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    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]

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  14. class ReferencePosition extends ReferenceRegion

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

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  16. class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

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  17. class ReferencePositionSerializer extends Serializer[ReferencePosition]

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  18. case class ReferenceRegion(referenceName: String, start: Long, end: Long, orientation: Strand = Strand.INDEPENDENT) extends Comparable[ReferenceRegion] with Interval with Product with Serializable

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    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]

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  20. class SAMFileHeaderWritable extends Serializable

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  21. class SequenceDictionary extends Serializable

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  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

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    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

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  24. class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

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  25. class SnpTable extends Serializable with Logging

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

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    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

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  28. class VariantContext extends AnyRef

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Value Members

  1. object Alphabet

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  2. object Coverage extends Serializable

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    Converts from avro Feature to Coverage.

  3. object MultiContigNonoverlappingRegions extends Serializable

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  4. object NonoverlappingRegions extends Serializable

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  5. object OptionalPositionOrdering extends OptionalReferenceOrdering[ReferencePosition]

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  6. object OptionalRegionOrdering extends OptionalReferenceOrdering[ReferenceRegion]

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  7. object PositionOrdering extends ReferenceOrdering[ReferencePosition]

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  8. object ProgramRecord extends Serializable

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  9. object ReadBucket extends Serializable

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  10. object RecordGroup extends Serializable

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  11. object RecordGroupDictionary extends Serializable

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  12. object ReferencePosition extends Serializable

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  13. object ReferencePositionPair extends Logging with Serializable

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  14. object ReferenceRegion extends Serializable

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  15. object RegionOrdering extends ReferenceOrdering[ReferenceRegion]

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  16. object SequenceDictionary extends Serializable

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    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]

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  18. object SequenceOrderingByRefIdx extends Ordering[SequenceRecord]

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  19. object SequenceRecord extends Serializable

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  20. object SingleReadBucket extends Logging with Serializable

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  21. object SnpTable extends Serializable

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  22. object TagType extends Enumeration

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  23. object VariantContext

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    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

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