[khmer-announce] Beta Testers Wanted for an Update to the khmer Software

[em at msu.edu]

Hi khmer Users,

During part of last year, we (Titus Brown's lab) made a number of  
changes to the khmer software. These changes were confined to a  
development branch of the source code and have not yet been released  
as the default "master version". The following is a list of some of  
the changes:

(*) Support was added for bzip2-compressed FASTA and FASTQ files.
(*) The FASTA and FASTQ parsers were rewritten for thread-safety and  
to provide a better-isolated software design. (The isolation has  
already paid off in that it preemptively fixed one bug that was  
recently reported to afflict the current master version of the  
software.)
(*) Some support for multithreaded operation was added and it scales  
decently (at least up to 8 cores - it has not been seriously  
benchmarked beyond that yet).
(*) The software's Python API has some new features, such as providing  
a screed-like Read class and direct access to the FASTA and FASTQ  
parsers.

We have performed some testing on these changes within the lab   but  
would like to receive feedback from the broader khmer community. We  
are still in the process of updating the documentation although  
nothing should have changed with the basic usage of scripts or  
existing programming interfaces. If you are feeling adventurous and  
would like to help us validate the changes for incorporation into the  
master version of khmer, then that would be appreciated. To get  
started with the "beta version", please clone a new repository with  
the following options or similar:

   git clone -b bleeding-edge  http://github.com/ged-lab/khmer.git khmer-BETA

Thanks!

P.S. Feedback via the GitHub issue trackers (  
https://github.com/ged-lab/khmer/issues ) is preferred for bug reports.