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  1. IGB
  2. IGBF-3464

Deploy htsjdk-igb

        Details

          Description

          Situation: In order to add CRAM file support (IGBF-1469) we need to update the HTSJDK dependency version. Currently we are using the artifact htsjdk-igb.

          Task: Investigate our use of the htsjdk-igb dependency. Determine how we can update this dependency.

          Github repo: https://github.com/lorainelab/htsjdk-igb

            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-1469 Investigate supporting CRAM files

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

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3465 Update BigWig/BigBed htsjdk-igb version

              • Major - Major loss of function.
              • Closed
              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1418 Import htsjdk as OSGi bundle

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3484 Update htsjdk-igb to 3.0.0

              • 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-1469 [ IGBF-1469 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-1418 [ IGBF-1418 ]
                nfreese Nowlan Freese made changes -
                Link This issue is blocked by IGBF-3465 [ IGBF-3465 ]
                nfreese Nowlan Freese made changes -
                Sprint Fall 3 2023 Oct 2 [ 179 ] Fall 4 2023 Oct 16 [ 180 ]
                nfreese Nowlan Freese made changes -
                Epic Link IGBF-1531 [ 17617 ] IGBF-3467 [ 22628 ]
                nfreese Nowlan Freese made changes -
                Description Situation: In order to add CRAM file support (IGBF-1469) we need to update the HTSJDK dependency version. Currently we are using the artifact htsjdk-igb.

                Task: Investigate our use of the htsjd-igb dependency. Determine how we can update this dependency.                 		Situation: In order to add CRAM file support (IGBF-1469) we need to update the HTSJDK dependency version. Currently we are using the artifact htsjdk-igb.

                Task: Investigate our use of the htsjd-igb dependency. Determine how we can update this dependency.

                Github repo: https://github.com/lorainelab/htsjdk-igb
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Link This issue blocks IGBF-3478 [ IGBF-3478 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16 [ 180 ] Fall 4 2023 Oct 16, Fall 5 [ 180, 181 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                kgopu Kaushik Gopu made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Kaushik Gopu [ kgopu ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Kaushik Gopu [ kgopu ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3484 [ IGBF-3484 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                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 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Kaushik Gopu [ kgopu ]
                nfreese Nowlan Freese made changes -
                Description Situation: In order to add CRAM file support (IGBF-1469) we need to update the HTSJDK dependency version. Currently we are using the artifact htsjdk-igb.

                Task: Investigate our use of the htsjd-igb dependency. Determine how we can update this dependency.

                Github repo: https://github.com/lorainelab/htsjdk-igb                 		Situation: In order to add CRAM file support (IGBF-1469) we need to update the HTSJDK dependency version. Currently we are using the artifact htsjdk-igb.

                Task: Investigate our use of the htsjdk-igb dependency. Determine how we can update this dependency.

                Github repo: https://github.com/lorainelab/htsjdk-igb
                nfreese Nowlan Freese made changes -
                Summary Investigate updating HTSJDK Investigate updating HTSJDK and deploying the artifact
                nfreese Nowlan Freese made changes -
                Summary Investigate updating HTSJDK and deploying the artifact Investigate updating/deploying htsjdk-igb
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16, Fall 5 [ 180, 181 ] Fall 4 2023 Oct 16, Fall 5, Fall 6 [ 180, 181, 182 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Summary Investigate updating/deploying htsjdk-igb Deploy htsjdk-igb
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                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 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Kaushik Gopu [ kgopu ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                kgopu Kaushik Gopu made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                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 -
                Assignee Kaushik Gopu [ kgopu ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Kaushik Gopu [ kgopu ]
                nfreese Nowlan Freese 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 4 2023 Oct 16, Fall 5, Fall 6 [ 180, 181, 182 ] Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7 [ 180, 181, 182, 183 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                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 -
                Assignee Kaushik Gopu [ kgopu ]
                pkulzer Paige Kulzer made changes -
                Fix Version/s 10.0.0 Major Release [ 10900 ]

                  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: