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  1. IGB
  2. IGBF-3478

Add CRAM support to IGB

        Details

        • Story Points:
          5
        • Epic Link:
        • Sprint:
          Fall 4 2023 Oct 16, Fall 6, Fall 7, Fall 8, Spring 1, Spring 2

          Description

          Task: Add CRAM file support to IGB.

          Task list:

          • Implement CRAM reference source
          • Implement CRAM file type handler
          • Implement CRAM methods(parse(), getSAMReader())
          • Load 2-bit data from code
          • Check the possibility of unit tests
          • Review the code
          • Test code with different input samples

          Working Branch

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3550 Add CRAM to list of supported files for BioViz Connect

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

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

              • Major - Major loss of function.
              • Closed

              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

              Task - A task that needs to be done. IGBF-3543 Rebase cram changes on main-JDK21-with-javafx-no-theme

              • 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-3467 [ 22628 ]
                nfreese Nowlan Freese made changes -
                Link This issue is blocked by IGBF-3465 [ IGBF-3465 ]
                nfreese Nowlan Freese made changes -
                Link This issue is blocked by IGBF-3464 [ IGBF-3464 ]
                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
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16, Fall 5 [ 180, 181 ] Fall 4 2023 Oct 16, Fall 6 [ 180, 182 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                kgopu Kaushik Gopu made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16, Fall 6 [ 180, 182 ] Fall 4 2023 Oct 16, Fall 6, Fall 7 [ 180, 182, 183 ]
                nfreese Nowlan Freese made changes -
                Story Points 3 5
                kgopu Kaushik Gopu made changes -
                Comment [ Task list:
                * Implement CRAM reference source(/)
                * Implement CRAM file type handler(/)
                * Implement CRAM methods(parse(), getSAMReader())(/)
                * Load 2-bit data from code (on)
                * Check the possibility of unit tests
                * Review the code
                * Test code with different input samples
                ]
                kgopu Kaushik Gopu made changes -
                Description Task: Add CRAM file support to IGB. Task: Add CRAM file support to IGB.

                Task list:
                * Implement CRAM reference source(/)
                * Implement CRAM file type handler(/)
                * Implement CRAM methods(parse(), getSAMReader())(/)
                * Load 2-bit data from code (on)
                * Check the possibility of unit tests
                * Review the code
                * Test code with different input samples
                kgopu Kaushik Gopu made changes -
                Description Task: Add CRAM file support to IGB.

                Task list:
                * Implement CRAM reference source(/)
                * Implement CRAM file type handler(/)
                * Implement CRAM methods(parse(), getSAMReader())(/)
                * Load 2-bit data from code (on)
                * Check the possibility of unit tests
                * Review the code
                * Test code with different input samples
                		Task: Add CRAM file support to IGB.

                Task list:
                * Implement CRAM reference source(/)
                * Implement CRAM file type handler(/)
                * Implement CRAM methods(parse(), getSAMReader())(/)
                * Load 2-bit data from code (on)
                * Check the possibility of unit tests
                * Review the code
                * Test code with different input samples

                [Working Branch | https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/cram_feature_wip]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16, Fall 6, Fall 7 [ 180, 182, 183 ] Fall 4 2023 Oct 16, Fall 6, Fall 7, Fall 8 [ 180, 182, 183, 184 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese 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 -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Kaushik Gopu [ kgopu ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16, Fall 6, Fall 7, Fall 8 [ 180, 182, 183, 184 ] Fall 4 2023 Oct 16, Fall 6, Fall 7, Fall 8, Spring 1 [ 180, 182, 183, 184, 185 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                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 ] 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 ]
                nfreese Nowlan Freese made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3543 [ IGBF-3543 ]
                nfreese Nowlan Freese made changes -
                Assignee Kaushik Gopu [ kgopu ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese 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 6, Fall 7, Fall 8, Spring 1 [ 180, 182, 183, 184, 185 ] Fall 4 2023 Oct 16, Fall 6, Fall 7, Fall 8, Spring 1, Spring 2 [ 180, 182, 183, 184, 185, 186 ]
                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 -
                Link This issue blocks IGBF-3550 [ IGBF-3550 ]
                nfreese Nowlan Freese made changes -
                Assignee Kaushik Gopu [ kgopu ]
                pkulzer Paige Kulzer made changes -
                Fix Version/s 10.0.0 Major Release [ 10900 ]
                nfreese Nowlan Freese made changes -
                Issue Type Task [ 3 ] New Feature [ 2 ]

                  People

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

                    • Created:
                      Updated:
                      Resolved: