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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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                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  fixed

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - fixed
                  Hide
                  Permalink
                  adam Adam Baxter (Inactive) added a comment - - edited

                  In the described workflow, the 1st BAM file no longer loads.
                  The 2nd BAM file loads when "Refresh Data" is clicked.
                  SVN Version: 7816

                  Show
                  adam Adam Baxter (Inactive) added a comment - - edited In the described workflow, the 1st BAM file no longer loads. The 2nd BAM file loads when "Refresh Data" is clicked. SVN Version: 7816
                  Hide
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                  adam Adam Baxter (Inactive) added a comment -

                  Ignore that. I wasn't zoomed in far enough for autoload to occur.

                  Show
                  adam Adam Baxter (Inactive) added a comment - Ignore that. I wasn't zoomed in far enough for autoload to occur.
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Micheal noted same bug again. Could you please double check it again.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Micheal noted same bug again. Could you please double check it again.
                  Hide
                  Permalink
                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  I could not reproduce this bug with the information given.... I tried on A Thal using our data. followed instructions exactly. Then tried zooming in, and out, tried refreshing after the autoload, switching the autoload/region in view status, many variations with no problem...

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - I could not reproduce this bug with the information given.... I tried on A Thal using our data. followed instructions exactly. Then tried zooming in, and out, tried refreshing after the autoload, switching the autoload/region in view status, many variations with no problem...
                  Hide
                  Permalink
                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9770 Windows

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9770 Windows
                  Hide
                  Permalink
                  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: