https://github.com/ngless-toolkit/interval-to-int
Interval map structure in Haskell designed for NGLess
https://github.com/ngless-toolkit/interval-to-int
interval-map
Last synced: about 2 months ago
JSON representation
Interval map structure in Haskell designed for NGLess
- Host: GitHub
- URL: https://github.com/ngless-toolkit/interval-to-int
- Owner: ngless-toolkit
- License: other
- Created: 2020-08-13T23:05:27.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2022-06-02T13:20:55.000Z (almost 3 years ago)
- Last Synced: 2024-04-23T21:33:33.646Z (about 1 year ago)
- Topics: interval-map
- Language: Haskell
- Homepage:
- Size: 42 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: ChangeLog
- License: COPYING
Awesome Lists containing this project
README
# IntervalIntMap
An interval map structure that is optimized for low memory (each interval is
represented by about 3 words + whatever the cargo is) and has semantics that
are appropriate for genomic intervals (namely, intervals can overlap and
queries will return **all** matches together). It also designed to be used in
two phases: a construction phase + query phase).
This is not a general purpose package, it serves mostly as support for
[NGLess](https://ngless.embl.de) and is used there.
Do get [in touch](mailto:[email protected]) if you want to use it more
generally, but the plans for this repo is to develop it only in so far as it
helps with NGLess' goals.
## Example Usage
### Step 1: construction
In the first phase, an `IntervalIntMapAccumulator` accumulator is used. This is
a mutable object and it must be used inside a `PrimMonad` (typically either
`IO` or `ST s`). Elements can be inserted into this object.
```haskell
import qualified Data.IntervalIntMap as IM
insertMany :: [(Int, Int)] -> IO (IM.IntervalIntMap Int)
insertMany elems = do
acc <- IM.new
forM_ (zip elems [0..]) $ \((s,p), ix) ->
IM.insert (IM.Interval s p) ix
IM.unsafeFreeze acc
```
The final step in _construction_ is freezing the accumulator to produce a
`IntervalIntMap`. If the original accumulator is not to be used again, then
`unsafeFreeze` can be used.
### Step 2: usage
The `IntervalIntMap` object is a pure object, with the typical container
functions: `map`, `lookup`, `elems`,...
Do note that the signature for `lookup` is
```haskell
lookup :: Storable a => Int -> IntervalIntMap a -> [a]
```
Thus, a list is always returned: `[]` if nothing is found, but multiple
intervals can independently overlap with the query.
## Citation
If you do use this repository, please cite the main [NGLess](https://ngless.embl.de) paper:
> _NG-meta-profiler: fast processing of metagenomes using NGLess, a
> domain-specific language_ by Luis Pedro Coelho, Renato Alves, Paulo Monteiro,
> Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork, Microbiome (2019)
> [https://doi.org/10.1186/s40168-019-0684-8](https://doi.org/10.1186/s40168-019-0684-8)
LICENSE: MIT