Hi Brad, thanks for your patch. Do you mind to create a pull-request to my github account? https://github.com/bgruening/galaxytools Otherwise, are you ok if I push it and reference you by name? Also, it would be good the make the non-sorting optional. Many of us using the calling program from methtools: https://github.com/bgruening/methtools And that requires a sorted BAM file to use multiple cores. Thanks for your work! Bjoern Am 08.04.2014 07:39, schrieb Langhorst, Brad:

This patch updates bjorn’s bismark wrapper to work with latest bismark and allows methylation extraction from SAM or BAM files. It no longer sorts the BAM from bismark (to allow methylation extraction to work).