Hi,

I added some functionality to deal with gzipped input and solved some compiler errors in this pull request. This introduces an extra dependency to zlib and adds an external library that is downloaded automatically when compiling. Detailed changelog is included below.

Thanks for publishing this tool - I almost started implementing my own before stumbling upon yours :)

Changelog

Add support for using gzipped files as input (resolves #12).

• Supported via the bxzstr library which replaces std::ifstreams in the code with bxz::ifstream. (commit aa09a3c)
• bxzstr is downloaded automatically when running cmake. The version of bxzstr is set at a fixed commit in config/CMakeLists-bxzstr.txt.in. (commit ce6ef2e)
• zlib is now a required dependency when building but it should be available on all systems that process genome data anyway. (commits 9283d38 and 3dad1b1)
• Also supports reading files compressed with bzip2 and lzma if they are present on the system when compiling. Bzip2 and lzma are not required for building and support for them is detected and set automatically when running cmake.

Fixed compiler errors that happened on some systems with specific versions of GCC and Linux. (commits 4e5f27c and 5d831e9)

Added tests for gzipped input. (commit de201f0)