Add benchmarking mode (resolves #101) #107
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Added: * FreeBayes * Platypus * 16GT * Strelka (and Manta) * Samtools Mpileup/BCFtools call Also, ported over GATK3 HaplotypeCaller from toil-scripts.
…rking-mode Conflicts: src/toil_lib/tools/preprocessing.py
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Adds the ability to return runtimes from individual job invocations. I call this benchmarking mode, because I plan to use it in a pipeline that runs a plethora of these tools and generates accuracy and timing plots.
Not ready for merge yet; this is also where I'll be doing misc cleanup.