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  1. IGB
  2. IGBF-3465

Update BigWig/BigBed htsjdk-igb version

        Details

        • Story Points:
          3
        • Epic Link:
        • Sprint:
          Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7

          Description

          Situation: The BigWigHandler and BigBedHandler have a dependency on the artifact bigWigHandler (https://bitbucket.org/lorainelab/bigwig/src/master/). The bigWigHandler dependency has a dependency on htsjdk-igb version 2.16.2 which makes it a blocker for IGBF-3464.

          Task: Fork the bigwig repo and create a new branch with htsjdk-igb updated to a newer version (most likely >= 3). You will need to build and test the dependency locally to make sure that IGB works. See this documentation on adding local jars to local m2 repository.

            Attachments

              Issue Links

              blocks

              New Feature - A new feature of the product, which has yet to be developed. IGBF-3478 Add CRAM support to IGB

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3464 Deploy htsjdk-igb

              • Major - Major loss of function.
              • Closed
              is blocked by

              Task - A task that needs to be done. IGBF-3490 Import HTSJDK 3.0.5 as OSGI bundle

              • Major - Major loss of function.
              • Closed

                Activity

                  People

                  • Assignee:
                    kgopu Kaushik Gopu
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: