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Using the toolkit
Tutorial available here. It is a work-in-progress, but should soon provide helpful tips on getting the most out of the command-line suite.
In order to discover compilation and linking flags, BamTools now also installs a pkg-config file bamtools-1.pc. Using pkg-config is recommended over second guessing -I and linking flags. Furthermore, the pkg-config file is versioned by major API for forwards compatibility. A major API break will lead to us bumping the pkg-config file to bamtools-2.pc and also changing the library name to bamtools-2.so, in order to allow side-by-side installation with the older BamTools.
A tutorial on how to use pkg-config in various build systems can be found in the GTest documentation: https://github.com/google/googletest/blob/master/googletest/docs/Pkgconfig.md