Start of 64 bit genome locations
A little more work on longer genome locations
Mork work toward 64 bit genome locations.  Doesn't build, just a checkpoint.
Compiles, haven't run it yet
ran once
Merge branch 'dev' into bill
bugfix
Worked once for index build & single end (plus, found a bug in the old code & fixed it)
More work on 64 bit support
More 64 bit tweaking, plus include single or paired on the command line in @PG
Fix comma syntax, which broke when I added single or paired to the @PG line
version to merge back into dev
1.0dev.28: 64 bit genome location support