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https://github.com/sstadick/lapper.cr
Crystal port of nim-lapper: a fast genomic intervals query library
https://github.com/sstadick/lapper.cr
algorithms bioinformatics crystal intervals
Last synced: about 1 month ago
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Crystal port of nim-lapper: a fast genomic intervals query library
- Host: GitHub
- URL: https://github.com/sstadick/lapper.cr
- Owner: sstadick
- License: mit
- Created: 2020-05-22T14:50:36.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2020-05-24T15:52:31.000Z (over 4 years ago)
- Last Synced: 2024-08-05T14:15:36.267Z (5 months ago)
- Topics: algorithms, bioinformatics, crystal, intervals
- Language: Crystal
- Homepage: https://sstadick.github.io/lapper.cr/
- Size: 44.9 KB
- Stars: 5
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
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[](https://sstadick.github.io/lapper.cr/)
# lapper.cr
This is a Crystal port of Brent Pendersen's [nim-lapper](https://github.com/brentp/nim-lapper). This crate works well for most genomic interval data. It does have a notable worst case scenario when very long regions engulf large percentages of the other intervals. As usual, you should benchmark on your expected data and see how it works.
## Documentation
See [here](https://sstadick.github.io/lapper.cr/)
## Installation
1. Add the dependency to your `shard.yml`
```yml
dependencies:
lapper:
github: sstadick/lapper.cr
```
## Usage
```crystal
require "lapper"
# Create some fake data
data = (0..100).step(by: 20).map { |x| Lapper::Interval(Int32).new(x, x + 10, 0) }.to_a
# Create the lapper
lapper = Lapper::Lapper(Int32).new(data)
# Demo `find`
lapper = Lapper::Lapper(Int32).new(data)
lapper.find(5, 11).size == 2
# Demo `seek` - calculate overlap between queries and the found intervals
sum = 0
cursor = 0
(0..10).step(by: 3).each do |i|
sum += lapper.seek(i, i + 2).map { |iv| Math.min(i + 2, iv.stop) - Math.max(i, iv.start) }.sum
end
puts sum
```
## Performance
Has not yet been benchmarked for the Crystal implementation. For other languages this library outperforms [all implementations](https://github.com/sstadick/rust-lapper#benchmarks) when the intervals are not heavily nested. For another Crystal implementation of an interval lib, see [klib.cr](https://github.com/lh3/biofast/blob/master/lib/klib.cr), which is based on the [cgranges](https://github.com/lh3/cgranges) lib by the same author.
### Bench against klib
Benchmarked against the klib.cr implementation and using the script found in `bench/biofast.cr` (uses the `find` with block method).
```text
Benchmark #1: ./bedcov_c1_cgr -c ../biofast-data-v1/ex-rna.bed ../biofast-data-v1/ex-anno.bed > bedcov_c1_cgr.out
Time (mean ± σ): 3.221 s ± 0.128 s [User: 3.091 s, System: 0.122 s]
Range (min … max): 3.075 s … 3.423 s 10 runs
Benchmark #2: ./bedcov_cr1_klib ../biofast-data-v1/ex-rna.bed ../biofast-data-v1/ex-anno.bed > bedcov_cr1_klib.out
Time (mean ± σ): 8.045 s ± 0.223 s [User: 5.457 s, System: 2.688 s]
Range (min … max): 7.764 s … 8.440 s 10 runs
Benchmark #3: bedcov_cr1_lapper/bin/bedcov_cr1_lapper ../biofast-data-v1/ex-rna.bed ../biofast-data-v1/ex-anno.bed > bedcov_cr1_lapper.out
Time (mean ± σ): 9.591 s ± 0.116 s [User: 6.966 s, System: 2.751 s]
Range (min … max): 9.498 s … 9.835 s 10 runs
Summary
'./bedcov_c1_cgr -c ../biofast-data-v1/ex-rna.bed ../biofast-data-v1/ex-anno.bed > bedcov_c1_cgr.out' ran
2.50 ± 0.12 times faster than './bedcov_cr1_klib ../biofast-data-v1/ex-rna.bed ../biofast-data-v1/ex-anno.bed > bedcov_cr1_klib.out'
2.98 ± 0.12 times faster than 'bedcov_cr1_lapper/bin/bedcov_cr1_lapper ../biofast-data-v1/ex-rna.bed ../biofast-data-v1/ex-anno.bed > bedcov_cr1_lapper.out'
```
### `find` and `seek` variants on query data sorted by start
```text
find 13.86 ( 72.17ms) (± 8.03%) 81.5MB/op 1.63× slower
seek 15.31 ( 65.33ms) (± 4.51%) 81.5MB/op 1.48× slower
find_yield 21.95 ( 45.57ms) (± 5.29%) 1.53MB/op 1.03× slower
seek_yield 22.61 ( 44.23ms) (± 1.52%) 1.53MB/op fastest
find_share 15.36 ( 65.08ms) (± 3.68%) 81.5MB/op 1.47× slower
seek_share 15.52 ( 64.43ms) (± 4.30%) 81.5MB/op 1.46× slower
```
Note that for more queries than represented here, `seek` should get faster.
The `bench\bench.cr` script is expecting the [this](https://github.com/lh3/biofast/releases/download/biofast-data-v1/biofast-data-v1.tar.gz) data to be in the top top level dir of the repo and untarred.
## Contributing
1. Fork it ()
2. Create your feature branch (`git checkout -b my-new-feature`)
3. Commit your changes (`git commit -am 'Add some feature'`)
4. Push to the branch (`git push origin my-new-feature`)
5. Create a new Pull Request
## Contributors
- [Seth Stadick](https://github.com/sstadick) - creator and maintainer