reference

Type Members

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

   

   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. implicit final class ContigLengths extends AnyVal

   

3. implicit final class ContigName extends AnyVal with Serializable with Ordered[ContigName]

   

4. trait ContigSequence extends BasesBuffer

   

5. class ContigsIterator[T] extends SimpleBufferedIterator[(ContigName, ContigIterator[T])]

   

   Divide an iterator into a series of contig-restricted iterators.

   Divide an iterator into a series of contig-restricted iterators.

   Takes an iterator of arbitrary elements and a function for extracting a ContigName from them.

   Emits ContigIterator) tuples.

   See companion object for public constructors.

6. trait HasContig extends Any

   

7. trait HasLocus extends Any

   

8. trait Interval extends Any

   

9. type KmerLength = Int

   

10. implicit final class Locus extends AnyVal with Ordered[Locus] with Comparable[Locus]

    

11. type NumLoci = Locus

    

12. case class Position(contigName: ContigName, locus: Locus) extends Region with HasLocus with Product with Serializable

    

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

13. trait Region extends HasContig with Interval

    

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

14. class Registrar extends KryoRegistrator

    

15. case class RepeatedContigException(msg: String) extends Exception with Product with Serializable

    

16. case class Slice(contigName: ContigName, start: Locus, bases: Bases) extends Region with Product with Serializable

    

17. implicit final class WindowSize extends AnyVal with Ordered[Int]