Hi Greg,

On Mon, Nov 18, 2013 at 4:02 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> On Nov 18, 2013, at 10:33 AM, Peter Cock <p.j.a.c...@googlemail.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.

Peter
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