white space changes
updted $PS1 to prevent garbled cmdline
removed DefineSets
now passed @ARGV to main
corrected minor typos and bugs before testing
removed some comments
change to operate as a unfunneled fan i.e. dataflows to accumulated idr_peak_counts array
updated AddPeakDataSets to use -analysis_name to prevent analysis_top_up bug, upped the memory pwm_mapping
Change can run analysis param names to omit "run". Changed set type case to match class case. Removed DefineReplicateDataSet. Change SubmitIDR to PreprocessIDR. Added run_SWEmbl_R0005_replicate.
Now handles creating merged IDR rep ResultSet and merge_bams
Now uses class case for set types. Also handles ids and names as inputs. Lot's of other changes to handle input_subsets
some typos and small bug fixes
Now uses sam_header and merge_bams methods. added flow-mode support for signal or replicate