Tumour only calling using FreeBayes falls back to single sample mode
Calculate fastqc name to find after downsampling to ensure we correctly find files in downsampling applied. Fixes #512
Avoid division by zero error in cpat (fixes #517). Cleanly avoid running cpat if not installed
vcfallelicprimitives applied to paired FreeBayes output
Added FreeBayes tumor-only test
Avoid doing merging of input variant_regions BED files until required. Enables passing initial full files with extra fields through to VarDict and other callers that require them. Thanks to @mjafin @bioinfo
Merge pull request #518 from mjafin/freebayes

Tumour only calling using FreeBayes falls back to single sample mode