[Bioc-devel] Announcing availability of Rhtslib package
nhayden at fredhutch.org
Mon Mar 9 22:52:27 CET 2015
On 03/09/2015 01:34 PM, Moritz Gerstung wrote:
> Cool beans, I have been hoping that this would happen!
> Does that mean that Rsamtools will slowly be phased out, and packages linking to Rsamtools should switch to Rhtslib? [Which I wanted to do anyways to be able to use CRAM.]
Yes! That's exactly the idea. New packages using samtools functionality
should be developed using Rhtslib, and maintainers of existing packages
should move to linking against [HTSlib in] Rhtslib. The samtools library
source and associated libraries (libbam.a, libbcf.a, libtabix.a) will be
removed from Rsamtools. Rsamtools will itself link to Rhtslib. Thanks
> On 9 Mar 2015, at 18:36, Nathaniel Hayden <nhayden at fredhutch.org> wrote:
>> Correction: Rhtslib contains version 1.1 of HTSlib.
>> On 03/09/2015 10:59 AM, Nathaniel Hayden wrote:
>>> I'm pleased to announce the availability of the Rhtslib package (http://bioconductor.org/packages/devel/bioc/html/Rhtslib.html , https://github.com/nhayden/Rhtslib), which provides the new-and-improved next generation of the samtools library: HTSlib (http://www.htslib.org/ , https://github.com/samtools/htslib). samtools is the C library that powers Rsamtools and related packages that manipulate and analyze SAM/BAM and VCF/BCF files, and interact with tabix files.
>>> Rhtslib currently includes version 1.0 of HTSlib, but work is already underway to update to 1.2.1 (https://github.com/samtools/htslib/releases/tag/1.2.1)
>>> One notable achievement in Rhtslib is the availability of HTSlib on Windows. At the time of this writing, the upstream version of HTSlib is not available for Windows without the use of a Unix-like emulation environment (e.g., Cygwin). Making HTSlib available for Windows via Rhtslib was possible with the use of Gnulib - The GNU Portability Library (https://www.gnu.org/software/gnulib/), which addresses portability problems by importing "modules" of portability source code into a repository on an as-needed basis.
>>> Rhtslib currently provides HTSlib as a static library on all platforms, but dynamic library versions will soon be available for Linux and Mac OS X. The static library will likely remain the sole option for Windows because the dynamic version requires the availability of a system pthreads DLL.
>>> Please let me know of any issues you encounter.
>>> Nathaniel Hayden
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