org.hammerlab.guacamole.distributed

RegionsByContig

class RegionsByContig[R <: ReferenceRegion] extends AnyRef

Using an iterator of regions sorted by (contig, start locus), this class exposes a way to get separate iterators over the regions in each contig.

For example, given these regions (written as contig:start locus): chr20:1000,chr20:1500,chr21:200

Calling next("chr20") will return an iterator of two regions (chr20:1000 and chr20:1500). After that, calling next("chr21") will give an iterator of one region (chr21:200).

Note that you must call next("chr20") before calling next("chr21") in this example. That is, this class does not buffer anything -- it just walks forward in the regions using the iterator you gave it.

Also note that after calling next("chr21"), the iterator returned by our previous call to next() is invalidated.

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Instance Constructors

  1. new RegionsByContig(regionIterator: Iterator[R])

    regionIterator

    regions, sorted by contig and start locus.

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  14. final def ne(arg0: AnyRef): Boolean

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  15. def next(contigName: ContigName): Iterator[R]

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