Incomplete beginning of ClipOverlapResult (mostly pasted from
    InstrumentData::Gatk::Base
Stub in _run_clip_overlap
Added content to _run_clip_overlap
Added a RefineReads/ClipOverlap module
changed BamUtils to the correct BamUtil
wrappers for BamUtil and its clipoverlap tool
test for clipoverlap
test for BamUtil base class
Clean up commented out code
removed unused property
Added a passing test for ClipOverlapResult. Minor adjustments in the .pm
to improve the test.
Remove unnecessary require
ClipOverlapResult calls _prepare_staging_directory and now the test
passes with only overriding the tool execute and bam_path.
clean up RefineReads/ClipOverlap.pm to work with ClipOverlap instrument data
Remove commented code
Added comments
Added reference_build to params_for_result. RefineReads::ClipOverlap works now and has a test.
Allow refiners without known_sites. Also allow multiple refiners.
Trying to test new/multiple refiners. Test does not pass yet
add leaf definition to allow nested refines. Tests pass