Bio-MAF 1.0.1 is released! As described in my last post, this includes support for BGZF-compressed MAF files and a command-line maf_extract(1) tool exposing almost all of the library’s random access functionality in an orthogonal way from the command line. It also includes a substantial overhaul of the maf_tile(1) tool, adding a --concat option for concatenation of several tiled intervals. This supports one of the original motivating use cases for this library, enabling alignments corresponding to a set of exons to be concatenated and any gaps filled from a reference sequence. The resulting output corresponds to their mRNA product.

Several other new maf_tile options support integration into Galaxy.

Since my last post, I have also made substantial performance improvements in BGZF compression and exercised the parser and indexing functionality on the entire set of UCSC multiz46way MAF files. This led to better memory management, handling of extended-range UCSC bins in indexing, better logging and warning generation, index version validation, index error reporting, and other work to make this library more robust and useful.

Sadly, this is the end of the Google Summer of Code. I’ve enjoyed working on Bio-MAF, getting to know the BioRuby community and especially my fantastic mentors, and most of all, delivering a useful piece of bioinformatics software. Thanks also to Google for organizing and funding this!

While the Summer of Code is over, I plan to continue to maintain Bio-MAF. While the originally envisioned feature set has been implemented, I will at least keep it up to date with dependencies. And, of course, if you use this library or are considering it, please file Github issues (or, better yet, pull requests) for any bugs, problem reports, feature requests, or suggestions you may have.