0.17

• human split with no target align (secondary stage) template introduced
• initial work for stage one (bcl, adapter, phiX and spatial filter to split processing) using templates
• bammarkduplicates reintroduced for unaligned file because downstream qc processing relies on presence of markdups_metrics file
• library cram merging: merge_aligned.json and merge_final_output_prep.json
• remove potential deadlock by using non-blocking open of STDIN