Setup now gets and installs bwa
Finished up tests for compile_reads
Fixing stuff. Why was build in the repo?
Added more useful returns for index_ref
Had to change how BWAIndex deals with its hackish way around the output file for times when it is run in a multiprocessor environment as the output file would be identical for all processes and be deleted by one process and the rest would raise an OSError exception because they tried to delete an already deleted file
Merging in Github dev branch
Fixed a few merge issues and added install section to README