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Add timings to README.
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gusevfe committed Jul 16, 2014
1 parent 7ac3ba4 commit d7f3173
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10 changes: 9 additions & 1 deletion README.md
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Ruby bindings for a very fast FASTA/Q parser [kseq.h](https://github.com/lh3/seqtk/blob/master/kseq.h) by Heng Li.

A default FASTA/Q parser from [BioRuby](http://bioruby.org) is extremly slow. One alternative is to use [bio-faster](https://github.com/fstrozzi/bioruby-faster) but that lacks support for FASTA files.
A default FASTA/Q parser from [BioRuby](http://bioruby.org) is extremly slow. One alternative is to use [bio-faster](https://github.com/fstrozzi/bioruby-faster) but that lacks support for FASTA files. However, `bio-faster` does parse qualities, unlike `bio-kseq`.

## Timings
```
user system total real
BioRuby 2.130000 0.270000 2.400000 ( 2.403145)
Bio::Faster 0.420000 0.070000 0.490000 ( 0.486809)
Bio::Kseq 0.030000 0.010000 0.040000 ( 0.037176)
```

## Installation

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4 changes: 3 additions & 1 deletion bio-kseq.gemspec
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Expand Up @@ -23,6 +23,8 @@ Gem::Specification.new do |spec|

spec.add_development_dependency "bundler", "~> 1.5"
spec.add_development_dependency "rake"
spec.add_development_dependency "rspec" ">= 3.0.0"
spec.add_development_dependency "rspec", ">= 3.0.0"
spec.add_development_dependency "rake-compiler"
spec.add_development_dependency "bio" # For timing script
spec.add_development_dependency "bio-faster" # For timing script
end

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