On 2015-08-12 17:20, David Roazen wrote:
> htsjdk (https://github.com/samtools/htsjdk/ [1]), and software built on top > of it such as the GATK, currently only support BAI indices with CRAM files. > It also appears likely that when CRAI support is added to htsjdk, it will be > implemented internally as an on-the-fly CRAI -> BAI conversion. > > So, there is a bit of a need right now for samtools index -b <cram_file> to > honor the "-b" option and create a BAI index on a CRAM file. Or a need for GATK to start supporting CRAI. I'm not yet convinced that abusing BAI to index something with a non-32k (or is it 64k?) block size format is the best way to go. Admittedly though I haven't investigated how it works as initially I just assumed it would be impossible. CRAM isn't a bgzf stream so I didn't explore further. I think it does something like treat containers as reads instead, but I'm not sure on practically what that means for index efficiency. Links: ------ [1] https://github.com/samtools/htsjdk/ -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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