map

Type Members

1. case class Contig[T](name: ContigName, rangeMap: RangeMap[Locus, T]) extends TruncatedToString with Product with Serializable

   

   A map from loci to instances of an arbitrary type where the loci are all on the same contig.

   A map from loci to instances of an arbitrary type where the loci are all on the same contig.

   name

   The contig name

   rangeMap

   The range map of loci intervals -> values.

2. class ContigSerializer[T] extends com.esotericsoftware.kryo.Serializer[Contig[T]]

   

   We serialize a Contig as its name, the number of ranges, and the ranges themselves (two longs and a value each).

3. case class LociMap[T](map: SortedMap[ContigName, Contig[T]]) extends TruncatedToString with Product with Serializable

   

   An immutable map from loci to a instances of an arbitrary type T.

   An immutable map from loci to a instances of an arbitrary type T.

   Since contiguous genomic intervals are a common case, this is implemented with sets of (start, end) intervals.

   All intervals are half open: inclusive on start, exclusive on end.

   map

   Map from contig names to Contig instances giving the regions and values on that contig.

4. class Serializer[T] extends com.esotericsoftware.kryo.Serializer[LociMap[T]]

   

   We serialize a LociMap simply by writing out all of its Contigs.