Le 27/07/2011 10:17, Peter Cock a écrit :
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.

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.

Ah ok, I understand!

It should be fine though, since we won't need to load bam files anymore shortly. Thanks for all the information!

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