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Using samtools C libraries with Rsamtools Martin Morgan Modified: 20 March, 2015. Compiled: February 23, 2020 Contents 1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2 Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2.1 Discover header files . . . . . . . . . . . . . . . . . . . . . . . 2 2.2 Link to static libraries . . . . . . . . . . . . . . . . . . . . . . . 2 This is meant for package developers w g to use the samtools C libraries provided by Rsamtools. The instructions here are based on the ‘Writing R Extensions’ associated with R-2.13; consult the current version of the for up-to-date instructions. 1 Background Rsamtools arranges to install static versions of the libbam and libbcf libraries. The idea is that other packages can use these to implement C functionality that uses these libraries. This means that the samtools libraries are available in a consistent version to users across tforms, without requiring installation of additional software. Rsamtools takes the following approach. On installation, Rsamtools contains a snapshot of the samtools library source code under src/samtools. Rsamtools makes static version(s) of the samtools libraries libbam.a and libbcf.a. These static libraries are specific to the _ operating system on which Rsamtools is being installed, are found under usrlib${R ARCH} in the user library loca