This package provides version 1.18 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 3.3.1
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 1.18.
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.See the Rsamtools package
for an example of a package that compiles and links against Rhtslib.
In order for the C/C++ compiler to find HTSlib headers during installation
of your package, you must add Rhtslib to the LinkingTo field of its
DESCRIPTION file, e.g.,
LinkingTo: RhtslibNote 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 "htslib/hts.h". Header files are available for perusal at (enter
in an R session)
system.file(package="Rhtslib", "include")## [1] "/tmp/RtmpVeNmu3/Rinst1213597f461d88/Rhtslib/include"To compile and link your package successfully against the HTSlib included
in Rhtslib, you must include a src/Makevars file.
Create a src/Makevars file with the following lines
RHTSLIB_LIBS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \
'Rhtslib::pkgconfig("PKG_LIBS")')
RHTSLIB_CPPFLAGS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \
'Rhtslib::pkgconfig("PKG_CPPFLAGS")')
PKG_LIBS=$(RHTSLIB_LIBS)
PKG_CPPFLAGS=$(RHTSLIB_CPPFLAGS)Note that $(shell ...) is GNU make syntax so you should add GNU make
to the SystemRequirements field of the DESCRIPTION file of your package,
e.g.,
SystemRequirements: GNU makeThe reason we use $(shell echo ...) rather than back-ticks (e.g.
`echo ...`) is because the latter causes problems when, after
evaluation, PKG_LIBS and/or PKG_CPPFLAGS contain paths with
whitespaces in them.
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 -lfoocomment: # This can cause problems, e.g., when the ‘head’ node of
comment: # a cluster mimicks the cluster node via a symbolic link to
comment: # the directory in which Rhtslib is installed. Use the
comment: # environment variable RHTSLIB_RPATH to resolve this by
comment: # setting it to the cluster-node accessible path.
Rhtslib provides both static and dynamic library versions of HTSlib
on Linux and Mac OS X platforms, but only the static version on
Windows. The procedure above will link against the static library
version of HTSlib on all platforms.