Linux fixes
More Linux fixes
Merge branch 'MAPQ-matei' of github.com:amplab/snap into MAPQ-matei
Remove large test data files
Fix flow control in RangeSplitter file input
Remove large regression test datafiles
Merge branch 'MAPQ-matei' of github.com:/amplab/snap into MAPQ-matei
Put ValidateSamFile.jar in with data
Merge branch 'MAPQ-matei' of https://github.com/amplab/snap into MAPQ-matei
Write BAM index file
Handle headerless SAM files
Fix BAM linear index
Tweak BAM index format
fast paired end more, mode instrumentation, -B option
Merge with Ravi's changes
Compile on Linux
Merge branch 'MAPQ-matei' of https://github.com/amplab/snap into MAPQ-matei
0.16alpha.0: change paired end -h default to 2000, min spacing to 50