lapper.cr

This is a Crystal port of Brent Pendersen's 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

Installation

1. Add the dependency to your shard.yml

dependencies:
  lapper:
    github: sstadick/lapper.cr

Usage

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 when the intervals are not heavily nested. For another Crystal implementation of an interval lib, see klib.cr, which is based on the 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).

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

      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 data to be in the top top level dir of the repo and untarred.

Contributing

1. Fork it (https://github.com/sstadick/lapper.cr/fork)
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 - creator and maintainer