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
Diagnostic stats for PairedReadMatcher
Merge branch 'dev' of https://github.com/amplab/snap into dev
Reducing allocation in PairedReadMatcher - in progress
merge
merge
PairedReadMatcher WIP
PairedReadMatcher overflow alloc/free
New refcount design for data batches WIP
merge
More refcount WIP
Buffer count calculations for refcounting
Turn off debug printouts
merge
Adjust buffer counts
merge
Move unneeded files back to snap2
Add stdin/stdout to filetest.py
Merge branch 'dev' of https://github.com/amplab/snap into dev