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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