Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3698

Fix right-click Filter... in IGB when track is separated into (+) and (-) strands

        Details

        • Type: Bug
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: IGB users can use the right-click Filter... option in IGB to filter annotations or reads in a track based on properties such as score. However, there is a bug where if the track is separated by strand and the filter is applied to one strand and then removed in the other strand, the data do not reappear.

          Task: Fix it so that if a filter is applied to a strand it can only be removed from that strand.

          To reproduce the issue:

          1. Start IGB
          2. Select the Arabidopsis genome
          3. Navigate to Chr1:8,673,056-8,677,891
          4. Right-click on the Araport track and select Filter...
          5. In the Filter menu, select Add
          6. In the Add filter menu, select Show Only Score
          7. Click OK
          8. Click OK
          9. The gene model in the Araport track should now be hidden
          10. Right-click on the Araport track and select Filter...
          11. Select the Score filter and click on the Remove button
          12. Click OK
            The filter should now be removed, but the gene model in the Araport track is still missing.

            Attachments

              Issue Links

              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3640 Add expand color by and Filter by to include the props

              • Major - Major loss of function.
              • In Progress

                Activity

                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited
                1. Open the most recent chicken genome (G_gallus_Mar_2018).
                2. Navigate to 1:79,200,818-79,317,139
                3. Under UCSC REST in the Data Access tab under Available Data, select cpgIslandExt
                4. Load Data
                5. Right-click on the cpgIslandExt track label and select Filter...
                6. Click Add
                7. Set Show Only to Score
                8. Set score to 10.0 and comparator to >=
                9. Click OK
                10. Click OK

                The following error appears:

                Apr 18, 2024 10:18:44 AM com.affymetrix.igb.action.FilterAction applyFilter
WARNING: Found a glyph with null info at location java.awt.geom.Rectangle2D$Double[x=0.0,y=53.764827058823535,w=0.0,h=20.0]
                Show
                nfreese Nowlan Freese added a comment - - edited Open the most recent chicken genome (G_gallus_Mar_2018). Navigate to 1:79,200,818-79,317,139 Under UCSC REST in the Data Access tab under Available Data, select cpgIslandExt Load Data Right-click on the cpgIslandExt track label and select Filter... Click Add Set Show Only to Score Set score to 10.0 and comparator to >= Click OK Click OK The following error appears: Apr 18, 2024 10:18:44 AM com.affymetrix.igb.action.FilterAction applyFilter WARNING: Found a glyph with null info at location java.awt.geom.Rectangle2D$ Double [x=0.0,y=53.764827058823535,w=0.0,h=20.0]

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    1 Start watching this issue

                    Dates

                    • Created:
                      Updated: