Jeremiah Wala

Can you provide the full ./configure command you are providing? Your arguments to --with-bamtools aren't being seen by configure. From my config.log: ``` configure:5895: checking api/BamReader.h usability configure:5912: g++ -c...

Hmm, this is puzzling. Perhaps something in the way autotools is building the configure script? If you do `./configure --help` do you see the `with-bamtools` options? Otherwise, can you try...

Hmm, I'm stumped, I don't know why even the attached configure isn't working. As a work around, I think you can just comment out the bamtools check of configure.ac and...