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  1. Bug Repository
  2. BUG-94

NPE when refreshing BAM track - ID: 3237699

          Details

          • Type: Bug
          • Status: Closed (View Workflow)
          • Priority: Major
          • Resolution: Fixed
          • Labels:
            None

            Description

            This seems to happen reliably following these steps:

            • Zoom in to some gene
            • Load a BAM and set to Auto Load
            • Load another BAM, leave to Refresh Data
            • Click Refresh Data

            This appears:
            Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
            at com.affymetrix.igb.view.load.GeneralLoadUtils.checkBamLoading(General
            LoadUtils.java:760)
            at com.affymetrix.igb.view.load.GeneralLoadUtils.loadAndDisplaySpan(Gene
            ralLoadUtils.java:671)
            at com.affymetrix.igb.view.load.GeneralLoadUtils.loadAndDisplayAnnotatio
            ns(GeneralLoadUtils.java:650)
            at com.affymetrix.igb.view.load.GeneralLoadView.loadFeatures(GeneralLoad
            View.java:621)
            at com.affymetrix.igb.view.load.GeneralLoadView.loadVisibleFeatures(Gene
            ralLoadView.java:589)
            at com.affymetrix.igb.action.RefreshDataAction.actionPerformed(RefreshDa
            taAction.java:32)

              Attachments

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-651 Windows specific bugs

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

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                  5 older comments
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                  anuj Anuj Puram (Inactive) added a comment -

                  Passed version 6.7.0 (9791) on Mac

                  Show
                  anuj Anuj Puram (Inactive) added a comment - Passed version 6.7.0 (9791) on Mac
                  Hide
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                  smylapur Vineeth Mylapur (Inactive) added a comment - - edited

                  As of the above Description It doesn't show any Exceptions.

                  But now change the zoom cursor to after threshold and now scroll the bar.

                  It throws Null Pointer Exception

                  Show
                  smylapur Vineeth Mylapur (Inactive) added a comment - - edited As of the above Description It doesn't show any Exceptions. But now change the zoom cursor to after threshold and now scroll the bar. It throws Null Pointer Exception
                  Hide
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                  anuj Anuj Puram (Inactive) added a comment -

                  could not reproduce it on r11936
                  Please test it again

                  Show
                  anuj Anuj Puram (Inactive) added a comment - could not reproduce it on r11936 Please test it again
                  Hide
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                  smylapur Vineeth Mylapur (Inactive) added a comment -

                  Works Fine.
                  Tested with pollen.mm.bam and drought_control_2.mm.bam from http://transvar.org/illumina/tophat_2_processed/

                  Passed 7.0 (11940) on windows.

                  Show
                  smylapur Vineeth Mylapur (Inactive) added a comment - Works Fine. Tested with pollen.mm.bam and drought_control_2.mm.bam from http://transvar.org/illumina/tophat_2_processed/ Passed 7.0 (11940) on windows.
                  Hide
                  Permalink
                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Is this more of a windows bug?

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Is this more of a windows bug?

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      michafla Michael Lawrence (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: