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.
Diagnostic stats for PairedReadMatcher
Merge branch 'dev' of https://github.com/amplab/snap into dev
Ensure batches are released for dropped reads
Merge branch 'dev' of https://github.com/amplab/snap into dev
1.0dev.3: Add interleaved paired FASTQ input format, explicit file typing, new app to turn S/BAM into FASTQ
Fix merge conflicts
Fix build breaks (different ones on Windows and Linux)
1.0dev.4: Add -om option to write secondary alignments
Merge
Fix paired fastq command line parsing
Secondary alignment fixes
Merge branch 'dev' of github.com:amplab/snap into dev
Pieces of stdio input/output.  Doesn't even compile, just committing to allow local merge.
Reducing allocation in PairedReadMatcher - in progress
Fix dropped batch counting