[Bioc-devel] Announcing availability of Rhtslib package
nhayden at fredhutch.org
Mon Mar 9 19:36:52 CET 2015
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
> 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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