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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

                Ascending order - Click to sort in descending order
                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1531 [ 17617 ]
                nfreese Nowlan Freese made changes -
                Link This issue blocks IGBF-3464 [ IGBF-3464 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Story Points 3
                nfreese Nowlan Freese made changes -
                Epic Link IGBF-1531 [ 17617 ] IGBF-3467 [ 22628 ]
                ann.loraine Ann Loraine made changes -
                Attachment IMG_3751.jpg [ 18056 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 3 2023 Oct 2 [ 179 ] Fall 3 2023 Oct 2, Fall 4 2023 Oct 16 [ 179, 180 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Link This issue blocks IGBF-3478 [ IGBF-3478 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 3 2023 Oct 2, Fall 4 2023 Oct 16 [ 179, 180 ] Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5 [ 179, 180, 181 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5 [ 179, 180, 181 ] Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5, Fall 6 [ 179, 180, 181, 182 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                kgopu Kaushik Gopu made changes -
                Link This issue is blocked by IGBF-3490 [ IGBF-3490 ]
                kgopu Kaushik Gopu made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                kgopu Kaushik Gopu made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                kgopu Kaushik Gopu made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                kgopu Kaushik Gopu made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                kgopu Kaushik Gopu made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                kgopu Kaushik Gopu made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                kgopu Kaushik Gopu made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                kgopu Kaushik Gopu made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                kgopu Kaushik Gopu made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                kgopu Kaushik Gopu made changes -
                Assignee Kaushik Gopu [ kgopu ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5, Fall 6 [ 179, 180, 181, 182 ] Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7 [ 179, 180, 181, 182, 183 ]
                nfreese Nowlan Freese made changes -
                Assignee Kaushik Gopu [ kgopu ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 10.0.0 Major Release [ 10900 ]
                nfreese Nowlan Freese made changes -
                Issue Type Task [ 3 ] Improvement [ 4 ]

                  People

                  • Assignee:
                    kgopu Kaushik Gopu
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: