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interval

Unit Tests Coverage Status Language

A better genomic interval that is compatible with HTSJDK.

[Snoqualmie Mountain, Washington]

val interval = Interval("chr1", start = 1, end = 2, name = "MyInterval")
interval.sameCoordinates(interval) shouldBe true
interval.asHtsJdk.getContig shouldBe "chr1"

Features

  • The Interval is a 1-based fully closed span upon a reference sequence
  • Each Interval magically mixes in HTSJDK's Interval while hiding the HTSJDK API
  • The HTSJDK API can be summoned by casting the Interval with .asHtsJdk()
  • Implicit conversions allow for seamless interoperability between either Interval class
  • Grants you a memory-friendly way of having a Scala-esque API upon HTSJDK's Interval

If Mill is your build tool

ivyDeps ++ Agg(ivy"io.cvbio.coord::interval::0.0.1")

If SBT is your build tool

libraryDependencies += "io.cvbio.coord" %% "interval" % "0.0.1"