I have released bio-maf version 0.2.0 as a Ruby gem. The main new feature in this release is MAF ‘tiling’; combining the alignment blocks covering a given genomic interval, optionally filling in gaps with reference sequence data, to output a single alignment block. See the README for more details. This includes a maf_tile(1) tool. The name of this feature, and inspiration for the implementation, comes from the bx-python implementation.

This release also enables gap removal in cases where removal of some species from an alignment block leaves a gap in all remaining sequences.

Other fixes and improvements include:

• #59: returning blocks in sorted order
• #56: avoiding a race condition in parallel parsing
• Using all available cores by default under JRuby