Thanks for getting back to me so quickly James!
If I used the test_view program directly, would that give me a reasonable
sense of runtime and compression performance?
Also, is there a release schedule for samtools? When is the next release
planned?
On Wed, Jul 1, 2015 at 1:47 AM, James Bonfield <[email protected]> wrote:
> 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;
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> formae,
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>
>
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