Original duplicates now built-in without needing special build args - #112
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…ector when duplication words to be counted need to be initialized for original dups
…n of duplicates to count in original duplicates mode
…al dups alongside new dups analysis method; aiming to have both side-by-site
…processer var ORIGINAL_DUPS and keeping both code side-by-site
…on run_mode for original_dups
…n purely to facilitate original_dups mode and moving the initialization of results_collector objects per thread into the threads themselves to avoid any waiting for all the init to happen sequentially
…nalysis with a flag; performance uncertain
…al dups mode without building for it
…d reads when identifying the duplication set for original duplicates
…e one in bam_file and likely it's too large. If we hit 2x then we know the duplication should fail
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