[Open-bio-l] Bio::Faster update version 0.4.4

[Pjotr Prins]

Brilliant. If I see this correctly, Francesco has also written a new
C parser, pretty much overnight.

Pj.

On Fri, Apr 27, 2012 at 04:40:37PM +0200, Francesco Strozzi wrote:
> Hi all,
> I have updated the Bio::Faster gem for BioRuby. This gem allows for a
> fast parsing of FastQ files and it's based on a C extension.
> Many updates were done since the last version. The gem has been
> completely rewritten, both the C extension and the Ruby code. The C
> extension is now called through FFI, so this new gem works fine also
> with alternative Ruby interpreter, like JRuby.
> In particular, this new version can handle correctly the formatting
> errors that may be present in FastQ files, something that was not
> possible with the previous version due to the external C library used
> at the time.
> The RSpecs to build this new version were defined using the test files
> available from the official FastQ format paper
> (http://nar.oxfordjournals.org/content/38/6/1767.abstract).
> 
> The code is available here: https://github.com/fstrozzi/bioruby-faster
> The new version of the gem is available on RubyGems: gem install bio-faster
> 
> If you have the chance, please check this new version at let me know
> of any bugs or problems you may find.
> 
> Please note that since version 0.4.0 bio-faster does not support
> parsing FastA files anymore. The code is now only focused on FastQ
> format.
> 
> Cheers
> 
> -- 
> 
> Francesco
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>