On Wed, Aug 12, 2015 at 12:20:13PM -0400, David Roazen wrote: > htsjdk (https://github.com/samtools/htsjdk/), and software built on top of > it such as the GATK, currently only support BAI indices with CRAM > files.
Have you tested that they work? I don't seem able to get this working right now, but maybe I'm doing something wrong (or perhaps they have corner cases which fail). I was trying to see how they're implemented and how hard it is to implement (or indeed whether it's even a good idea). [At the very least we wouldn't want BAI and should switch to CSI, as we don't want CRAM to replicate the same limitations that BAM has.] James -- James Bonfield ([email protected]) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- 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. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
