[GSoC] bio-maf release 0.3.0

[Clayton Wheeler]

Hi all,

I've released bio-maf version 0.3.0:

http://csw.github.com/bioruby-maf/blog/2012/07/18/bio-maf_0.3.0/

This version adds features including joining adjacent MAF blocks when
sequences that caused them to be split have been filtered out;
returning bio-alignment objects; and truncating (or ‘slicing’)
alignment blocks to only cover a given genomic interval.

For developers, this also adds a higher-level Bio::MAF::Access API for
working with directories containing indexed MAF files (or,
alternatively, single files), providing all relevant functionality for
indexed access in a simpler way than using the KyotoIndex and Parser
classes directly. The maf_tile(1) utility has been updated to use this
functionality; a directory of indexed MAF files can now be specified,
and the correct file will now be parsed as appropriate.

Usage of Enumerators and blocks has also been substantially improved;
all access methods for multiple blocks such as Access#find,
Access#slice, Parser#each_block now accept a block parameter, which
will be called for each block in turn. If no block parameter is given,
they will all return an Enumeratorfor the resulting blocks. This is
how most of the Ruby standard library, e.g. Array#each, works.

--
Clayton Wheeler
cswh at umich.edu