DP assembly and depletion pipelines

Finish up assembly and depletion pipelines (snakemake), convert depletion pipeline to split up data into pieces prior to most of the work. Now all steps should be executable on the Broad "hour" queue. Toolify Samtools and Picard further, add some basic testing, convert snakemake pipelines to use the tool'ed versions of them. Clean some code and tests.  #23 #24 #30