
Steps to create your own mappability files:

- Download the fa files you want (one per chromosome), and put them in a directory, making sure that they end in '.fa'.  

- Make the three executables chr2hash, oligoFindPLFFile, mergeOligoCounts, using the Makefile.  
Make sure they are in your PATH.

- In the directory containing the fa files, do: python compile.py.  

You'll end up with pairs of files for each <chrname>.fa.HashOffsetTable, <chrname>.fa.HashPosTable

Then, use CountMap.py in the usual way to access the data.

