set total snps before looking up recombinations
if theres no recombination bases return the number of snps outside recombination
Merge pull request #98 from andrewjpage/stats_missing_snps

Stats missing snps
Moved definition of print_usage to before its first use.
Removed the external dependencies from the build
  - these are deps of the Python wrapper, not libgubbins.so.
Removed some autogenerated files.
Removed more autogenerated files and updated build documentation.
Modified the README to point at the INSTALL file for build instructions.
Added initial plumbing to get a configured Ubuntu 13.10 VM for release builds.
Added minimial number of control files for a valid Debian package.
libgubbins depends on libm, not just the gubbins binary.
Make -lrt explicit for the tests (for POSIX timers).
Build and configuration changes needed to build a gubbins .deb package.
Copy the .changes, .dsc and possibly modified .tar.gz to the build host.
Use cp to /vagrant rather than scp
  - SCP likes to check the host key of our temporay VM, and won't
    connect if it has seen localhost:2222 before (which it probably
    has).
Updated Debian build number to unclude a PPA string.
Added setup.py to the make
Streamlining the Debiab/Ubuntu package release
  - Use @PACKAGE_*@ autoconf vars
  - generate some debian/* files
Updated package dependancy list to include some of the python deps.
Made RaXML a recommended package, not a dependency,
since standard-raxml will be built if it is not found.
Also, some HPC facilities have customised builds of RaXML
so it is not ideal to make the binary package a strict dependency.