Changed directory structure and added version option

This version is really just a tidying exercise - but with important changes to the directory structure:

The piggy executable is now in piggy/bin
The other scripts are now in piggy/scripts_piggy

I have also deleted a few old scripts - piggy_old and piggy_divergence_plotter

There is now a version option (--version|-v)

I have also updated the installation instructions in the readme

Updated fix to core IGR alignment

This is a better fix for the core IGR alignment.

added size options, speedup

There is now a --size|-s option, this allows the size range of IGRs to be specified, for example:

--size 20-600

to only include IGRs between 20 and 600 bp in length.

I have also increased the speed of the previous fix for the temp files. It is now much faster.

Fewer temp files

Previously, Piggy produced a huge number of temporary files. I have written a quick fix to stop this, and so it should work on more isolates than before. It is a bit slower as a consequence, but I will improve the fix in the future.

Fix core IGR alignment

I have fixed a pretty major bug which affected the core IGR alignment. Previously, some sequences were masked with Ns instead of being added to the alignment. This didn't introduce erroneous SNPs, but meant that fewer SNPs were in the resulting alignment. Use this version!

First go

v1.0

Update README.md