On Mon, Nov 18, 2013 at 4:02 PM, Greg Von Kuster firstname.lastname@example.org wrote:
On Nov 18, 2013, at 10:33 AM, Peter Cock email@example.com wrote:
On a closely related point, I understand Galaxy likes to store all BAM files co-ordinate sorted and indexed - when a tool produces a BAM file where does this happen? i.e. Is it the individual tool's responsibility, or the framework (e.g. during setting metadata). I am assume the later, in which case is there still an implicit samtools dependency there?
This is (unfortunately) performed in multiple methods in the Bam class methods in ~/galaxy/datatypes/binary.py. There are some comments (pasted here) that include an old "TODO" in the Bam class's dataset_content_needs_grooming() method that clarifies some of the reasons for this: ...
Thanks for confirming that - I'll keep that in mind if I run into any BAM/BAI issues with my work on the MIRA4 and CLCbio wrappers which include BAM output.