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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
