Updated `genome` tab completion.
Updated `gmt` tab completion.
Add bwa-0.7.3a
refactor locking code

Pull locking code into separate function.  Same code is used in several
modules so it still isn't completely refactored.  Will fix that next.
Moving towards fixing the fact that locks shouldn't contain
subdirectories.
also get new lock

The old lock includes subdirectories and should not.  In order to
transition to a new lock scheme we currently have to lock both schemes.
Later we can remove the old scheme.
add diagnostics
make test pass even if UR_COMMAND_DUMP_STATUS_MESSAGES is set

Since test depends on status messages not being shown we should also set
$ENV{UR_COMMAND_DUMP_STATUS_MESSAGES} to 0 in case the tester has that
enabled.
whitespace
pull in Test::More master @ 74efe123
apply bugfix from Test::More 1.5 that hasn't been pulled into 0.98
update to use Test::More's subtest
remove sub_test since we can now use Test::More's subtest
remove _subtest since we can now use Test::More's subtest
Merge branch 'test_more'
Allow both gzipped and non gzipped vcfs as input
Merge branch 'master' into gb_master
Increase bwamem memory rusage
Modify Bwa memory request for certain ref builds

Some reference sequence builds will consistently cause Bwa to reach its
LSF memory limit. The AlignReads Event now provides the reference
sequence build when calling the aligner module's required_rusage method.
Bwa will now double the memory requirement from 8 to 16 GB when the
provided reference sequence build matches a build that we have
determined requires more memory.
load Test::* after 'use above' so we our Test::*
add diag to help reproduce failure on apipe-ci