On Tue, Jun 30, 2015 at 11:32:18PM -0700, Jeffrey Tratner wrote: > I saw on the release notes for htslib that it supports CRAM v3.0. Is there > any way to force samtools v1.2 to output v3 CRAM as opposed to v2.1? If > so, is support for CRAM v3.0 considered to be "production-ready"?
Sort of! The format is considered ready, but isn't well supported in the current official release. The test_view program in htslib has -o option to specify output options. This can control, amongst other things, the format version. Eg: test_view -o VERSION=3.0 -C foo.bam > foo.cram Htslib also exposes these options as a library, but the Samtools 1.2 implementation did not expose them to the command line. There is a pull request against a recent develop branch that adds --input-fmt, --output-fmt, --input-fmt-option and --output-fmt-option long opts to all samtools commands. (Incidentally this means we can use --output-fmt-option nthreads=8 to get multi-threaded BAM encoding on all commands, rather than just those supporting -@.) https://github.com/samtools/samtools/pull/395 Also I believe the develop branch of htslib/samtools now defaults to version 3.0, so the above pull request isn't necessary if you only ever want one version of CRAM. 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. ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
