https://github.com/clintval/interval

A better genomic interval that is compatible with HTSJDK
https://github.com/clintval/interval

coordinate genomics interval scala

Last synced: 8 days ago
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A better genomic interval that is compatible with HTSJDK

• Host: GitHub
• URL: https://github.com/clintval/interval
• Owner: clintval
• License: mit
• Created: 2022-01-21T16:08:23.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2022-01-22T03:19:15.000Z (over 4 years ago)
• Last Synced: 2026-04-28T22:35:17.386Z (about 1 month ago)
• Topics: coordinate, genomics, interval, scala
• Language: Scala
• Homepage:
• Size: 3.01 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# interval

[![Unit Tests](https://github.com/clintval/interval/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/clintval/interval/actions/workflows/unit-tests.yml)

[![Coverage Status](https://codecov.io/gh/clintval/interval/branch/main/graph/badge.svg)](https://codecov.io/gh/clintval/interval)

[![Language](https://img.shields.io/badge/language-scala-c22d40.svg)](https://www.scala-lang.org/)

A better genomic interval that is compatible with [HTSJDK](https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/Interval.html).

![[Snoqualmie Mountain, Washington]](.github/img/cover.jpg)

```scala

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

```scala

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

```

#### If SBT is your build tool

```scala

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

```