Fix Visual Studio compiler errors.

Fix Visual Studio compiler errors.

Don't use dynamic stack allocation (variable length arrays).
Rename bamtools target to bamtools_cmd to not conflict with BamTools target (they differ only in case).
bamtools_cmd only compiles if I remove bamtools_filter.cpp, which I haven't committed.
I also had to manually configure the include directory for zlib,
but that's probably due to having multiple copies floating around my machine.