[GSoC] Bio-MAF 1.0.1

[Clayton Wheeler]

Hi all,

I've released bio-maf 1.0.1 and written a final GSoC blog post about it:

http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/

This release should be substantially more robust, with solid and
reasonably-performing BGZF support, better CLI tools, and various
robustness, compatibility, and memory-footprint improvements.

(I've also developed a Galaxy integration for the maf_tile tool;
unlike the existing Galaxy MAF tools, this is capable of filling in
gaps with a FASTA reference sequence, and concatenating the alignment
output from several exons specified in a BED file. It's not quite all
packaged up with the toolshed facility yet, but I should be able to
wrap that up shortly. Sneak preview: https://gist.github.com/3418576)

It's been a pleasure working with all of you, and I'm glad I've been
able to deliver something useful. Pjotr, Raoul, Francesco, thanks for
your help and advice this summer! Marjan, Artem, you guys did
excellent work and gave me some great suggestions in the code reviews.
And, of course, thanks to Google for organizing and funding this!

-- 
Clayton Wheeler
cswh at umich.edu