Set library-type flag properly for Cufflinks runs.

Thanks to @paniccodewriter for the report. Fixes #487.
fix error when restart rnaseq and cufflinks is already done
Merge pull request #489 from lpantano/upstream

fix error when restart rnaseq and cufflinks is already done
Initial framework for automated evaluation of structural variant caller outputs based on known BED file of validated SVs
Ensure BAM merging following sample split so that blocked tumor/normal samples are both combined. Fixes #486. Provide checks for misplaced top level keys. Handle BED files with track inputs to cleanup functionality
Ensure paired tumor/normal varscan output does not have non-GATC allele calls. Fixes #491
Cleanly handle varscan cleaning case when line previously removed. #491
Produce validation CSV files for structural variant calls, avoiding comparisons in excluded low complexity regions. Avoid pre-calculating merging in complex regions which reduced sensitivity.
add kraken to QCsummary function