reference

Type Members

1. trait Contig extends BasesBuffer

   

2. 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.

3. implicit final class ContigLengths extends AnyVal

   

4. final class ContigName extends AnyVal with Serializable with Ordered[ContigName]

   

   Implicit-value-class wrapper for strings representing names of contigs.

   Implicit-value-class wrapper for strings representing names of contigs.

   Construction is controlled by the companion object, which uses an implicit org.hammerlab.genomics.reference.ContigName.Factory to decide whether to allow+collapse observed contig-names like "chr1" and "1" or throw an org.hammerlab.genomics.reference.ContigName.Strict.InconsistentContigNamesException; default behavior is the latter, but permissive handling can be enabled by importing org.hammerlab.genomics.reference.ContigName.Normalization.Lenient.

   Wrapped strings are interned.

5. class ContigNameSerializer extends Serializer[ContigName]

   

6. class ContigsIterator[T] extends hammerlab.iterator.SimpleIterator[(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.

7. trait HasContig extends Any

   

8. trait HasLocus extends Any

   

9. trait Interval extends Any

   

10. type KmerLength = Int

    

11. final class Locus extends AnyVal with Ordered[Locus] with Comparable[Locus] with Serializable

    

12. type NumLoci = Locus

    

13. class PermissiveRegistrar extends RegistrarI

    

14. 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.

15. trait Region extends HasContig with Interval

    

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

16. class Registrar extends RegistrarI

    

    Expose two registrars, one that does "strict" contig-name-consistency-checking, and another that doesn't.

    Expose two registrars, one that does "strict" contig-name-consistency-checking, and another that doesn't.

    In order for worker tasks to handle/create ContigNames consistently with the driver, the kryo serializers have to behave consistently.

17. abstract class RegistrarI extends KryoRegistrator

    

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

    

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

    

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