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  1. UGENE
  2. UGENE-1114

Estimation of memory required for one short read in the Genome Aligner

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 1.11
    • Fix Version/s: 1.12
    • Component/s: NGS
    • Labels:
      None
    • Tests Type:
      Untestable
    • Affect Type:
      Userdefined

      Description

      The memory required for one read was estimated as:

      void ReadShortReadsSubTask::run() {
      ...
      n*24 + sizeof(SearchQuery) + ONE_SEARCH_QUERY_SIZE + query->length() + query->getNameLength() + query->getQuality().qualCodes.length()
      ...
      }
      

      But this was not enough and bad_alloc occurred on big data samples. A temporarily fix was done to avoid this - it doubled the value.

      It is required to understand the reason of bad_alloc and fix the issue appropriately.

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              Assignee:
              shutov Shutov Ilya
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Artyom Savchenko
              Watchers:
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                Dates

                Created:
                Updated:
                Resolved: