fix the build tests for indel normalization
ClinSeq - add example lister command for somatic-validation tumor bams and update test results
Minor style changes in Bwasw.pm
updated ur submodule to 0a72847
Bwamem now handles RG tags + other changes

Bwamem will now stream output from bwa through AddReadGroupTag. Made
other miscellaneous fixes; some code style changes; attempted to clean
up logic a bit.
Fix typos in Bwamem.
always set ASSUME_SORTED for Picard GC bias calculations in BamQC
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
added code to plot mutation distance
Merge branch 'master' of ssh://git/srv/git/genome
updated help file
Don't do logging in the debugger.

Logging has exits. Makes debugging pointless.
Allow for variants to be supplied for refinement.
Add support for a "refiner" to be run at the end of the merge process.

For now this happens within the same command as merging and deduplication.
Eventually merge, deduplicate, and this refinment all should be made into
their own workflow.
Use the parent class of Merged results.