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
1.0beta.3: Increase batch count for Linux MemMapDataReader
Allow for DOS EOF character in FASTQ
Allow for additional sequence characters in FASTQ
Fix compile warning
Allow DOS line endings in FASTA on Linux
Merge branch 'dev'

Conflicts:
	apps/snap/Main.cpp
1.0beta.4 merge from dev
1.0dev.2: have PairedReadMatcher optionally quickly drop reads with no RNEXT.  Remove dynamic allocation from Read class.
Merge branch 'dev' of https://github.com/amplab/snap into dev
Add -F b option to filter on both mates of pair
Merge branch 'dev' of https://github.com/amplab/snap into dev

Conflicts:
	SNAPLib/PairedAligner.cpp
oops, last commit broke the quality in Read objects that have been copied.