On Wed, Mar 23, 2011 at 4:24 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hello Peter,
> On Mar 18, 2011, at 11:26 AM, Peter Cock wrote:
>> Having checked my BAM files with samtools, I can confirm they
>> don't have the SO header.
>> samtools view -H myfile.bam | grep "SO:"
>> They were generated with BWA in a split+merge pipeline to use
>> multiple cores. I support I could run samtools reheader on them...
>> but it would be nice to avoid that.
> Change set 5256:4acde9321b63 now includes more robust checking
> if a bam file is sorted.


> If using a version of samtools 0.1.13 or newer,
> an error condition occurs if attempting to index an unsorted bam file.
> We take advantage of this in our checks.

Yes, that is what Heng Li recently recommended on the samtools
mailing list.

>> Did you see Pierre's little C tool using the samtools API to do this?
>> http://plindenbaum.blogspot.com/2011/02/testing-if-bam-file-is-sorted-using.html
> Yes, however in testing, a 6.6GB BAM file took 138 seconds to check
> with the posted 'bamsorted' code that uses the SAMtools API and 128
> seconds to index with SAMtools, so we're using samtools for the check.

Given Heng Li's recommendation to use this as a check for being
indexed, I would do the same.

>>> The only disadvantage is that you need a new samtools for it to
>>> work on 100% of cases but that seems like a good choice moving
>>> forward.
>> Yes, since Galaxy will typically do sort the index anyway, it makes
>> sense to try and do the indexing immediately, and thus find out if
>> a sort is required or not.

I see that is still pending, but since indexing is quite fast, doing it
twice isn't the end of the world.

Do you think it is worth trying to reuse a provided BAI file when
linking to a BAM file rather than copying it into Galaxy?


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