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#119 sffToCA -skip_dedupe

Gatekeeper
closed
Jason Miller
Feature (48)
3
2010-05-01
2010-04-15
Jason Miller
No

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.

Discussion

  • Jason Miller
    Jason Miller
    2010-04-16

    • status: open --> pending
     
  • Jason Miller
    Jason Miller
    2010-04-16

    At least in CA version 6.1, the sffToCA command supports a -nodedupe option.

     
    • status: pending --> closed
     
  • This Tracker item was closed automatically by the system. It was
    previously set to a Pending status, and the original submitter
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