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  1. IGB
  2. IGBF-2901

Create bed file parser and demo class for genoviz-sdk

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10

          Description

          Create a bed file parser and corresponding demo class to visualize the parsed introns and exons data using any glyph within the genoviz library.

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              Issue Links

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              Task - A task that needs to be done. IGBF-2865 Investigate glyphs representing introns in older versions of IGB

              • Major - Major loss of function.
              • Closed

                Activity

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                karthik Karthik Raveendran created issue -
                karthik Karthik Raveendran made changes -
                Field Original Value New Value
                Epic Link IGBF-592 [ 15664 ]
                karthik Karthik Raveendran made changes -
                Link This issue blocks IGBF-2865 [ IGBF-2865 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23 [ 125 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13 [ 125, 126 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                karthik Karthik Raveendran added a comment - - edited

                Initially rendering the .bed file in the map would take up to 5 mins. After a few changes in the data structures used, string functions, and algorithm optimization, the time taken went down to close to 85 secs. Further improvement on the data structure used and repainting strategy has reduced the time to almost 60s. Investigating IGB code for further improvement.

                Show
                karthik Karthik Raveendran added a comment - - edited Initially rendering the .bed file in the map would take up to 5 mins. After a few changes in the data structures used, string functions, and algorithm optimization, the time taken went down to close to 85 secs. Further improvement on the data structure used and repainting strategy has reduced the time to almost 60s. Investigating IGB code for further improvement.
                karthik Karthik Raveendran made changes -
                Attachment Improved time.jpg [ 16776 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13 [ 125, 126 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27 [ 125, 126, 127 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27 [ 125, 126, 127 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Aug 10 [ 125, 126, 127, 128 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Hide
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                ann.loraine Ann Loraine added a comment -

                This appears to be done. Moving to Done.

                Show
                ann.loraine Ann Loraine added a comment - This appears to be done. Moving to Done.
                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 -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    karthik Karthik Raveendran
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                    Dates

                    • Created:
                      Updated:
                      Resolved: