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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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                  michafla Michael Lawrence (Inactive) created issue -
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                  hiralv Hiral Vora (Inactive) added a comment -

                  fixed

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - fixed
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Adam Baxter [ adam ]
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                  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
                  adam Adam Baxter (Inactive) made changes -
                  Assignee Adam Baxter [ adam ] Hiral Vora [ hiralv ]
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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.
                  adam Adam Baxter (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB6.5 [ 10010 ] Bug Repository [ 10030 ]
                  Key IGB-117 BUG-22
                  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.
                  hiralv Hiral Vora (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project Bug Repository [ 10030 ] IGB6.5 [ 10010 ]
                  Key BUG-22 IGB-165
                  Hide
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                  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...
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB6.5 [ 10010 ] Bug Repository [ 10030 ]
                  Key IGB-165 BUG-94
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  david David Norris (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ]
                  david David Norris (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  david David Norris (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Katharine Kubiak [ kkubiak ]
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9770 Windows

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9770 Windows
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Anuj Puram [ anuj ]
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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
                  anuj Anuj Puram (Inactive) made changes -
                  Assignee Anuj Puram [ anuj ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Vineeth Mylapur [ smylapur ]
                  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
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Vineeth Mylapur [ smylapur ]
                  Resolution Fixed [ 1 ]
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  Assignee Hiral Vora [ hiralv ]
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Anuj Puram [ anuj ]
                  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
                  anuj Anuj Puram (Inactive) made changes -
                  Assignee Anuj Puram [ anuj ] Alyssa Gulledge [ alyssa ]
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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.
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ]
                  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?
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-651 [ BUG-651 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]

                    People

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

                      • Created:
                        Updated:
                        Resolved: