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  1. UGENE
  2. UGENE-5981

GZ: RefSeq for CLARK

    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: virogenesis
    • Fix Version/s: 1.31
    • Component/s: NGS, Workflow
    • Labels:
    • Story Points:
      5
    • Epic Link:
    • Sprint:
      DEV-30-6, DEV-30-7, DEV-30-8-RELEASE, DEV-31-2, DEV-31-3, DEV-31-4
    • Affect Type:
      Userdefined

      Description

      Support the GZ format as input for CLARK. Make sure an archived multi-FASTA can also be processed (see UGENE-6010).

        Attachments

          Issue Links

          is blocked by

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-6010 Multi-FASTA: RefSeq for CLARK

          • Critical - Crashes, loss of data, severe memory leak.
          • Closed

            Activity

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            varlax Alexey Varlamov added a comment -

            Implemented GZ for reference data (i.e. used to build DB) + fixed most prominent performance bottlenecks.
            This part can be tested (clark rebuild is required).

            Show
            varlax Alexey Varlamov added a comment - Implemented GZ for reference data (i.e. used to build DB) + fixed most prominent performance bottlenecks. This part can be tested (clark rebuild is required).
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            dsukhomlinov Dmitrii Sukhomlinov added a comment - - edited

            Archived sequence doesn't pass in CLARK, when the same non-archived passes correctly

            Show
            dsukhomlinov Dmitrii Sukhomlinov added a comment - - edited Archived sequence doesn't pass in CLARK, when the same non-archived passes correctly
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            atiunov Aleksey Tiunov [X] (Inactive) added a comment -

            CLARK can process compressed files during the database building. It can't classify compressed reads now, there is another issue for this: UGENE-6041.

            Show
            atiunov Aleksey Tiunov [X] (Inactive) added a comment - CLARK can process compressed files during the database building. It can't classify compressed reads now, there is another issue for this: UGENE-6041 .

              People

              Assignee:
              atiunov Aleksey Tiunov [X] (Inactive)
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Dmitrii Sukhomlinov
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: