Ensure pybedtools and other utilities that generate temporary files from python use a local temporary directory. Fixes #94
Identify and report problematic BED file inputs where chromosome names do not match the reference. Fixes #94
Improvements to installation and upgrade: use anaconda package for IPython installation and drop dev requirements. Correctly identify and remove broken symlinks to main executable
Update VQSR suggested parameters for latest version of GATK. Avoid HaplotypeScore for GATK-Haplotype recalibration since that is used internally in the caller instead of exposed in the VCF
Avoid maxing out system memory with multicore processes by placing buffer. Update VQSR parameters for latest gatk-haplotype recommendations
Enable specific memory parameters for GATK VQSR, which demands extra memory. Pass requirements to top level resource management
Provide better exposure of program resources to top level cluster creation: expose GATK, snpEff and ensure considered