Start of new IO stack
More NewIO work
Kill dead files, more factoring of IO stack
Merge in master branch changes
Kill SimpleSAMWriter (it was dead code)
Just working, doesn't build
Merge in SAM changes from master
Merge branch 'master' into NewIO
Builds, haven't tried to run it yet
Works now for single ended, at least.
Now runs in one simple case
Worked once for paired end
Added throttle in queued version, auto selection, etc.
Support for multiple input files.  Didn't even try to compile it.
Now it builds.  Haven't tried to run it yet.
Ran once
More tuning, make huge pages a command line option
Builds, haven't tried to run
Fix up no-longer-true assumption
More MAPQ tweaks