A user asked for an option on our SFF pre-processor. The option would turn off the remove-duplicates functionality. The reason is that he uses a 3rd party de-dupe program. Also, he'd like to feed Newbler and CA the same inputs for comparison. (If we implement this, then it could be a runCA parameter. If so, then it should optionally turn off the post-overlap remove-duplicates functionality also.) One downside: it might encourage people to pre-process their SFF files before feeding them to Celera Assembler.
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