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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 created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2954 [ IGBF-2954 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2978 [ IGBF-2978 ]
                nfreese Nowlan Freese made changes -
                Summary Investigate bigBed chromosome synonyms logic Fix bigBed chromosome synonyms logic
                nfreese Nowlan Freese made changes -
                Story Points 1 3
                nfreese Nowlan Freese made changes -
                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: Investigate possible fixes for bigBed to use the chromosome synonyms logic.

                Note that this task relies on files and information from IGBF-2954                 		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
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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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

                Show
                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
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Summary Fix bigBed chromosome synonyms logic Investigate: bigBed chromosome synonyms logic
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 2021 Oct 11 - Oct 22 [ 131 ] Fall 5 2021 Oct 11 - Oct 22, Fall 6 2021 Oct 25 - Nov 5 [ 131, 132 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Rank Ranked lower
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 2021 Oct 11 - Oct 22, Fall 6 2021 Oct 25 - Nov 5 [ 131, 132 ] Fall 5 2021 Oct 11 - Oct 22, Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 19 [ 131, 132, 133 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 2021 Oct 11 - Oct 22, Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24 [ 131, 132, 133 ] Fall 5 2021 Oct 11 - Oct 22, Fall 6 2021 Oct 25 - Nov 5 [ 131, 132 ]
                ann.loraine Ann Loraine made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]

                  People

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

                    • Created:
                      Updated: