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
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
Any pointers to recent wrappers would be welcomed.
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