BFAST 0.6.4e has been released. This minor version change includes two new
A new option ("-z") in 'bfast postprocess' randomly places ambiguous reads
similar to other aligners. The mapping quality will remain zero to be
consistent but this could help improve the uniformity of coverage.
Thanks to Charles S., the MD tag in the SAM output now will match that of
the output of "samtools calmd", improving compatibility of the BFAST SAM
Thank-you to all who have submitted questions, found bugs (and submitted
easy to debug test cases), and the growing number of contributors of code.
As always, please send suggestions or questions.