2011/7/27 Louise-Amélie Schmitt <louise-amelie.schm...@embl.de>:
> Hello Jennifer,
>
> Aaaah so the grooming means creating the .bai file? Ok, I didn't know,
> thanks for the information. But that leaves me wondering why it is necessary
> to copy the data (unless the alignments are not sorted yet, which is
> possible knowing where the data comes from). I won't have much time left to
> look into it but if I can I'll let you know.
>
> Thanks,
> L-A

Sadly samtools sort doesn't set the header information, so it is not
enough to look at that to say if and how a SAM/BAM file is sorted.

I think what the Galaxy code does now is attempt to index the BAM file
(as a safe way to find out if is really is suitably sorted), and if that fails
sorts it by co-ordinate (which will make a new BAM file) and then
indexes the sorted version.

Peter

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