# Motivation and use of Rhtslib

# Motivation

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.

## 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 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.

## 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 during installation of your package, you must add `Rhtslib` to the `LinkingTo` field of its `DESCRIPTION` file, e.g.,

    LinkingTo: Rhtslib

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)

    system.file(package="Rhtslib", "include")

    ## [1] "/tmp/Rtmp9n2lay/Rinst6f366759ce2/Rhtslib/include"

## Compile and link against the library

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 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: # 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.