Improved memory handling: explicitly add in memory for system usage and keep fractional memory estimates. Intended to better work with restricted memory setups like SLURM scheduler and VMs
Improve test running with wrapper script: uses pre-installed version of nose local to installer provided Python and handles re-writing existing system configurations to use smaller test-specific genome data.
Ensure BAM indexes are up to date with BAM file, re-creating if not. Fixes #181. Provide better error reporting for problem lines when running BamIndexStats. Fixes #180
Correctly detect regions versus target BED files for FreeBayes. Avoid leaking internal changes in subset_variant_regions used to cleanly subset by regions