change refalign SoftwareResult->get to get_with_lock

this was an indirect call made by most (all?) refalign builds
make SoftwareResult->get noisy
Include both the indel validation list and the DV2 file if they exist.
Skip detect variants if strategies are undef
Skip IdentifyDnp if no snv_detection_strategy.
Skip Review Variants if no snv detection strategy is set
Merge branch 'validation' into gb_master
fixed path for cufflinks files
updates to samtools options
Use the currently-running intepreter rather than `perl`.
Now that the display name has fancy characters, be careful what we name files.
RepeatMasker annotation importer
First pass at repeatmasker annotation
Allow user to specify which columns are which in input format
Merge branch 'updated2' into gb_master
Change instrument data linkage to be more specific so UR doesn't complain.
Added a ValidateLargeIndels.pm to get to the underlying commands
Merge branch 'master' into gb_master
Refactor
FusionTranscripts requires orientation
Merge branch 'updated2' into gb_master
widen metric name