This package provides version 1.1 of the ‘HTSlib’ C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in this vignette.
Rhtslib 1.10.0
Rhtslib is an R package that provides the C HTSlib library for high-throughput sequence data analysis. The library provides APIs for creating, indexing, manipulating, and analyzing data in SAM/BAM/CRAM sequence files and VCF/BCF2 variant files. See the HTSlib website for complete details and documentation.
The Rhtslib package is primarily useful to developers of other R packages who want to use the HTSlib facilities in the C code of their own packages.
The version of the included HTSlib is displayed at package load time, but a user can also query the HTSlib version directly by calling Rhtslib:::htsVersion() in an R session. The current version of the package is 1.1.
Effort is made to update the included version of HTSlib with minor version releases from the HTSlib authors. If you notice the included HTSlib is older than the current minor release of HTSlib, please contact the Rhtslib maintainer.
There are several advantages to using Rhtslib, rather than requiring an explicit user system dependency on htslib directly.
Rhtslib means that your users (who are not always sophisticated system administrators) do not need to manually install their own library.htslib, so that you as a developer can rely on presence of specific features (and bugs!) rather than writing code to manage different library versions.There is an example package, link2Rhtslib, that demonstrates how reverse dependencies should link to Rhtslib.
To link successfully to the HTSlib included in Rhtslib a package must include both a src/Makevars.win and src/Makevars file. Note: the contents of src/Makevars.win and src/Makevars are almost identical, but not quite. Be careful of the differences.
Create a src/Makevars.win file with the following lines
RHTSLIB_LIBS=$(shell echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\
"${R_HOME}/bin/R" --vanilla --slave)
PKG_LIBS=$(RHTSLIB_LIBS)and a src/Makevars file with the following lines
RHTSLIB_LIBS=`echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\
"${R_HOME}/bin/R" --vanilla --slave`
PKG_LIBS=$(RHTSLIB_LIBS)The statement for each platfrom modifies the $PKG_LIBS variable. If your package needs to add to the $PKG_LIBS variable, do so by adding to the PKG_LIBS=$(RHTSLIB_LIBS) line, e.g.,
PKG_LIBS=$(RHTSLIB_LIBS) -L/path/to/foolib -lfooThe Linux implementation embeds the location of the hts library in the Rhtslib shared object via the compiler flag -Wl,rpath,path, where path is determined by system.file("lib", package="Rhtslib"). The path determined by system.file() is from .libPaths(), and has resolved symbolic links to their actual path. This can cause problems, e.g., when the ‘head’ node of a cluster mimicks the cluster node via a symbolic link to the directory in which Rhtslib is installed. Use the environment variable RHTSLIB_RPATH to resolve this by setting it to the cluster-node accessible path.
In order for the C/C++ compiler to find HTSlib headers (and zlib headers on Windows) during package installation, add Rhtslib and zlibbioc to the LinkingTo field of the DESCRIPTION file of your package, e.g.,
LinkingTo: Rhtslib, zlibbiocNote that as of R 3.0.2 LinkingTo values can include version specifications, e.g., LinkingTo: Rhtslib (>= 0.99.10).
In C or C++ code files, use standard techniques, e.g., #include "hts.h". Header files are available for perusal at (enter in an R session)
system.file(package="Rhtslib", "include")## [1] "/tmp/RtmpGxLhl2/Rinst2cd0116c5d69/Rhtslib/include"Rhtslib provides both static and dynamic library versions of HTSlib on Linux and Mac OS X platforms, but only the static version on Windows. In most cases, for Linux and Mac OS X the procedure above will link to the dynamic library version of HTSlib. Please let the maintainer know if you run into issues with this strategy.