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  1. UGENE
  2. UGENE-7367

"Generate sequence" utility is too slow

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 40
    • Component/s: None
    • Labels:
      None
    • Sprint:
      DEV-40-4
    • Affect Type:
      Userdefined

      Description

      I tried to generate large test sequences using Tools->Generate sequence menu to test memory overflow issues and found that it works incredibly slow and has 0 tests.

      The reasons why it works slow:

      1) Fasta file writer is very slow because it reads every FASTA line from the DBI.
      2) Random sequence generator algorithm is too slow: takes 6 seconds to generate 100mb on my computer in debug mode which is unacceptable for a such simple task.

      The task is to optimize these trivial places and add performance counters into the code.

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              Assignee:
              yalgaer Yuliya Algaer
              Reporter:
              yalgaer Yuliya Algaer
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: