parsing

Type Members

1. case class LociRange(contigName: ContigName, start: Locus, endOpt: Option[Locus]) extends ParsedLociRange with Product with Serializable

   

2. final case class LociRanges(ranges: Iterable[LociRange]) extends AnyVal with ParsedLoci with Product with Serializable

   

3. sealed trait ParsedLoci extends Any

   

   Representation of genomic-loci ranges that may be used to instantiate a org.hammerlab.genomics.loci.set.LociSet.

   Representation of genomic-loci ranges that may be used to instantiate a org.hammerlab.genomics.loci.set.LociSet.

   Constituent ranges can be open-ended, so a ParsedLoci is typically a short-lived intermediate representation between String representations of ranges (possibly originating from cmdline-flags or a file) and a org.hammerlab.genomics.loci.set.LociSet whose open-ended ranges have been "resolved" using contig-length information found in a BAM header.

   The two implementations are:

   • All: sentinel value representing all loci on all contigs.
   • LociRanges: a sequence of LociRanges denoting (possibly open-ended) genomic-intervals.

   Examples:

   • chr1,chrY
   • chr2:0-100
   • chr1:123-124,chr5:456-457
   • all

4. sealed trait ParsedLociRange extends AnyRef

   

   Representation of a genomic range as parsed from a cmdline-flag or file.

   Representation of a genomic range as parsed from a cmdline-flag or file.

   Example ranges:

   • chr2:10-20
   • chr3
   • chr4:100-
   • all
   • none