[Bioc-devel] Announcing availability of Rhtslib package

Nathaniel Hayden nhayden at fredhutch.org
Mon Mar 9 18:59:27 CET 2015


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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