Package

org.hammerlab.genomics

reference

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package reference

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Type Members

  1. class ContigIterator[+T] extends BufferedIterator[T]

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    Given some elements and a function for extracting a ContigName from them, return an iterator that is restricted to the given contig.

    Given some elements and a function for extracting a ContigName from them, return an iterator that is restricted to the given contig.

    See companion object for public constructors which automatically infer contigNameFn from the input type.

  2. type ContigLengths = Map[ContigName, NumLoci]

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  3. type ContigName = String

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  4. trait ContigSequence extends AnyRef

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  5. trait HasContig extends AnyRef

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  6. trait HasLocus extends AnyRef

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  7. trait Interval extends Ordered[Interval]

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  8. type Locus = Long

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  9. type NumLoci = Long

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  10. trait Position extends Region with HasLocus with PartiallyOrdered[Position]

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    Base trait for classes that logically exist at one genomic locus.

  11. trait Region extends HasContig with Interval

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    Trait for objects that are associated with an interval on a genomic contig.

  12. case class Slice(contigName: ContigName, start: Locus, bases: Seq[Byte]) extends Region with Product with Serializable

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Value Members

  1. object ContigIterator

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    Public ContigIterator constructors that infer the ContigName-function from the iterator-type T.

  2. object ContigName

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    Helpers for dealing with contig-name strings.

  3. object HasLocus

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  4. object Interval

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  5. object Position

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  6. object Region

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  7. package test

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