Golden Helix patches

[gaberudy]

These are completely optional, but I've made a number of patches to enable our utalization as bamtools as a library. I've tried to keep them in their own commits.

The patches consist of a number of changes:

1. Comiler fixes for various compilers (notably the 'u' literal for char values > 128 and removing the static const std:string member of exception class).

2. Allowing BamDeviceFactor to conduct my own Bam readers as well as make Http/Ftp reader support optional (if you don't include the .cpp/.h files, they won't be available)

3. Allowing for callback for each alignment during the index process. This allows us to build coverage data alongside the index in a single pass.

Thanks for continuing to support this great project!