Now compiles
Added BWA tentative wrapping
First implementation of aln_set_read
Return a version string; init and free options
Name changes and style issues
More glue implementation
fix whitespace
Ad hoc Makefile
Compiles and loads the reference (hard-coded path)

On the other hand, aln_set_read returns an error.
Rename Makefile
Fixed includes for .h in different dir
Build with BWA is user-specified path