Motivation and use of _Rhtslib_
In Rhtslib: HTSlib high-throughput sequencing library as an R package

Motivation

r Biocpkg("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 r Biocpkg("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.

HTSlib version

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 r (capture.output(Rhtslib:::htsVersion(), type="message")).

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 r Biocpkg("Rhtslib") maintainer.

Motivation

There are several advantages to using Rhtslib, rather than requiring an explicit user system dependency on htslib directly.

Using Rhtslib means that your users (who are not always sophisticated system administrators) do not need to manually install their own library.
Your application uses a defined version of 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.

Use

See the Rsamtools package for an example of a package that compiles and links against Rhtslib.

Find headers

In order for the C/C++ compiler to find HTSlib headers (and zlib headers on Windows) during installation of your package, you must add Rhtslib and zlibbioc to the LinkingTo field of its DESCRIPTION file, e.g.,

LinkingTo: Rhtslib, zlibbioc

Note 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)

{R headers} system.file(package="Rhtslib", "include")

Compile and link against the library

To compile and link your package successfully against the HTSlib included in r Biocpkg("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 make

The 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 -lfoo

comment: # H.P. - May 3, 2019: We've switched to static linking on comment: # Linux so this is no longer relevant. comment: # The Linux implementation embeds the location of the hts comment: # library in the Rhtslib shared object via the compiler comment: # flag -Wl,rpath,path, where path is determined by comment: # system.file("usrlib", package="Rhtslib"). The comment: # path determined by system.file() is from .libPaths(), comment: # and has resolved symbolic links to their actual path. comment: # 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.

Implementation notes

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.