[Bioc-devel] Announcing availability of Rhtslib package

Nathaniel Hayden 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:
> All,
> 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.
> Thanks,
> Nathaniel Hayden

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