Treat all non-ACTG characters in input like N
Update version number for Ravi's change
Handle DOS line endings on Linux
0.15.7: Add support for chromosome name clipping on index build
1.0beta.1: beta release - merge dev branch
Fix build on Mac OS X 10.9

- xmmintrin.h is broken here, so disabled _mm_prefetch on Apple
- Changed some uses of "unsigned _int64" or _uint64 as size_t
1.0beta.2: Fix MultiInputPairedReadSupplier
1.0dev.1: merge 1.0beta.2