Cool beans, I have been hoping that this would happen! Does that mean that Rsamtools will slowly be phased out, and packages linking to Rsamtools should switch to Rhtslib? [Which I wanted to do anyways to be able to use CRAM.]
Cheers Moritz On 9 Mar 2015, at 18:36, Nathaniel Hayden <[email protected]> wrote: > 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 > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
