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  1. Bug Repository
  2. BUG-16

Successive mismatch graph generation causes end of file exception

    Details

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

      OS X: 10.6
      Java: 1.6.0_24
      SVN IGB: 7816

      Description

      I'm unable to test this on multiple species as I have only Arabidopsis BAM files available to me.
      The problem still exists after preferences/cache cleared out.
      Directions:
      Datasource URL: http://test.bioviz.org/quickload/
      Load TAIR10 mRNA with the load mode "Whole Genome"
      Load "Treatment Drought 1" BAM file. Set load mode to "Region In View"

      Right click on "Treatment Drought 1" track header(?The thing on the left) and choose "Make Mismatch Graph"

      Maneuver to a gene annotation of choice and click the "Refresh Data" button.
      Maneuver to another area where you will need to load BAM data. Choose the "Refresh Data" button again.

      In the logs will be the following error:

      java.io.EOFException
      at java.io.RandomAccessFile.readInt(RandomAccessFile.java:725)
      at com.affymetrix.genometryImpl.MisMatchGraphSym.updateY(MisMatchGraphSym.java:139)
      at com.affymetrix.genometryImpl.SeqSymSummarizer.getMismatchGraph(SeqSymSummarizer.java:75)
      at com.affymetrix.igb.view.DependentData.createMisMatchGraph(DependentData.java:85)
      at com.affymetrix.igb.view.DependentData.createTier(DependentData.java:54)
      at com.affymetrix.igb.view.TrackView.updateDependentData(TrackView.java:267)
      at com.affymetrix.igb.featureloader.QuickLoad$1.doInBackground(QuickLoad.java:176)
      at com.affymetrix.igb.featureloader.QuickLoad$1.doInBackground(QuickLoad.java:160)
      at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
      at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
      at java.util.concurrent.FutureTask.run(FutureTask.java:138)
      at javax.swing.SwingWorker.run(SwingWorker.java:316)
      at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
      at java.lang.Thread.run(Thread.java:680)

      There is no outward sign anything went wrong in IGB.

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          Issue Links

            Activity

            adam Adam Baxter (Inactive) created issue -
            adam Adam Baxter (Inactive) made changes -
            Field Original Value New Value
            Assignee Ann Loraine [ aloraine ] Hiral Vora [ hiralv ]
            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            fixed

            Show
            hiralv Hiral Vora (Inactive) added a comment - fixed
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ] Adam Baxter [ adam ]
            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-130 BUG-16
            alyssa Alyssa Gulledge (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            david David Norris (Inactive) made changes -
            Assignee Adam Baxter [ adam ]
            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
            kkubiak Katharine Kubiak (Inactive) added a comment -

            Passed v9871 Windows

            Show
            kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9871 Windows
            kkubiak Katharine Kubiak (Inactive) made changes -
            Assignee Katharine Kubiak [ kkubiak ] Anuj Puram [ anuj ]
            Hide
            anuj Anuj Puram (Inactive) added a comment -

            Passed v9908 on MAC

            Show
            anuj Anuj Puram (Inactive) added a comment - Passed v9908 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 ]
            Resolution Fixed [ 1 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Resolved [ 5 ] Closed [ 6 ]
            Assignee Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            Hide
            alyssa Alyssa Gulledge (Inactive) added a comment -

            originally reported by Adam Baxter

            Show
            alyssa Alyssa Gulledge (Inactive) added a comment - originally reported by Adam Baxter
            alyssa Alyssa Gulledge (Inactive) made changes -
            Reporter Adam Baxter [ adam ] Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]
            smylapur Vineeth Mylapur (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            Assignee Vineeth Mylapur [ smylapur ]
            Hide
            smylapur Vineeth Mylapur (Inactive) added a comment -

            Passed 7.0 (11953) on windows.

            Show
            smylapur Vineeth Mylapur (Inactive) added a comment - Passed 7.0 (11953) on windows.
            smylapur Vineeth Mylapur (Inactive) made changes -
            Status Reopened [ 4 ] Resolved [ 5 ]
            Assignee Vineeth Mylapur [ smylapur ]
            Resolution Fixed [ 1 ]
            richard Richard Linchangco (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Resolved [ 5 ] Reopened [ 4 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Link This issue is blocked by BUG-639 [ BUG-639 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]

              People

              • Assignee:
                Unassigned
                Reporter:
                alyssa Alyssa Gulledge (Inactive)
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                Dates

                • Created:
                  Updated:
                  Resolved: