https://github.com/sstadick/scivs
Collection of Data Structures for working with genomic intervals
https://github.com/sstadick/scivs
algorithm bioinformatics scala scala-port
Last synced: 3 months ago
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Collection of Data Structures for working with genomic intervals
- Host: GitHub
- URL: https://github.com/sstadick/scivs
- Owner: sstadick
- License: mit
- Created: 2020-01-06T22:55:00.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-06-09T12:48:52.000Z (about 5 years ago)
- Last Synced: 2025-03-27T04:09:31.384Z (3 months ago)
- Topics: algorithm, bioinformatics, scala, scala-port
- Language: Scala
- Homepage:
- Size: 32.2 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://index.scala-lang.org/sstadick/scivs/scivs)
# scivs
This is a library containing Classes and helpers for working with
genomic intervals in Scala. Currently `Lapper` and `ScAIList` are
implemented, which are best in class in their respective niche's.
scivs = SCala InterVal Stores
## Lapper
This is a Scala port of the
[nim-lapper](https://github.com/brentp/nim-lapper). It is also inspired
by the rust port [rust-lapper](https://docs.rs/rust-lapper).
```scala
import scivs.scailist.ScAIList
import scivs.interval.Interval
val lapper = new Lapper((0 to 20 by 5).map(Interval(_, _ + 2, 0)).toList))
assert(lapper.find(6, 11).toList(0), Interval(5, 7, 0))
```
### Performance Characteristics
Fantastic for 'normal' genomic data where intervals are 'short' and
there isn't much nesting. Think Illumina PE reads. The `seek` method in
particular is very fast if you know that your queries will be in order.
## ScAIList
This is an implementation of the code from this
[paper](https://www.biorxiv.org/content/10.1101/593657v1). The major
change is that the number of component parts a list is broken into is
dynamic and not hardcoded.
### Performance Characteristics
This datastructure is good for nested intervals where long intervals
engulf many shorter intervals.
```scala
import scivs.scailist.ScAIList
import scivs.interval.Interval
val scailist = ScAIList((0 to 20 by 5).map(Interval(_, _ + 2, 0)).toList))
assert(scailist.find(6, 11).toList(0), Interval(5, 7, 0))
```
## Todo's
- Add benchmarks / substantiate the performance characteristics
- Compare against other libs out there?
- Add some of the helper methods for things like coverage etc
- Figure out how to make my package level docs show up in javadoc