set

Type Members

1. case class Contig(name: ContigName, rangeSet: RangeSet[Locus])(implicit factory: Factory) extends TruncatedToString with Product with Serializable

   

   A set of loci on a contig, stored/manipulated as loci ranges.

2. class ContigSerializer extends Serializer[Contig]

   

   Serialize a LociSet simply by writing out its Contigs.

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

   

   An immutable collection of genomic regions on any number of contigs.

   An immutable collection of genomic regions on any number of contigs.

   Used, for example, to keep track of what loci to call variants at.

   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

   A map from contig-name to Contig, which is a set or genomic intervals as described above.