[galaxy-dev] samtools pileup deprecated

Hi All,

Maybe I missed it on the list here, but it seems that for samtools the pileup command has been deprecated without backward compatibility from the more recent samtools packages... http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html

Did anyone rewrite some of the samtools tool wrappers for this....? I am currently testing whether the Bam->pileup command can be easily changed in the sam_pileup.py script. But some functionality has gone and some additional is there. It seems I am up-to-date with the latest wrappers in the galaxy_dist repository.

Any pointers to recent wrappers would be welcomed.

Alex