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  1. IGB
  2. IGBF-2979

Investigate: bigBed chromosome synonyms logic

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: Investigation of bigBed file loading issues found that the IGB bigBed parser does not appear to use the chromosome synonyms logic when loading a file.

          Task: Fix the IGB bigBed logic so that it uses the chromosome synonyms logic.

          Note that this task relies on files and information from IGBF-2954

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              relates to

              Task - A task that needs to be done. IGBF-2954 Investigate: why is loading bb (bigbed) and bigwig (bw) files so slow?

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-2978 Improve bigBed parsing

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese added a comment -

                I am currently investigating the following files:
                ChromosomeSynonymLookupImpl.java
                SynonymLookupService.java
                SynonymLookup.java
                GeneralLoadUtils.java
                BedSymloader.java
                BigBedSymLoader.java
                BigWigSymLoader.java
                BigBedSymLoader.java

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                nfreese Nowlan Freese added a comment - I am currently investigating the following files: ChromosomeSynonymLookupImpl.java SynonymLookupService.java SynonymLookup.java GeneralLoadUtils.java BedSymloader.java BigBedSymLoader.java BigWigSymLoader.java BigBedSymLoader.java

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated: