Rhtslib 1.12.1
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 1.7.
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("usrlib", 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/RtmppesGqP/Rinsta806eaecb2b/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.