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  1. Deep Backlog
  2. DB-145

Loading BED detail file while IGB is loading a genome causes concurrency issues in the form of java.lang.NumberFormatExceptions

    Details

    • Type: Bug
    • Status: Open (View Workflow)
    • Priority: Major
    • Resolution: Unresolved
    • Labels:
      None

      Description

      TO REPRODUCE: Using clean preferences and clearing the bundle cache start an IGB session. Timing is important here so I will be as detailed as possible. From the welcome screen select Blueberry and wait for tracks to load. As soon as tracks load you should notice that the loading bar in the bottom left is still in an indeterminate state. Quickly open a bed file (the one attached to this issue) The file will start to load and then IGB will start throwing many java.lang.NumberFormatExceptions

      here is the last one on the list of many

      java.lang.NumberFormatException: For input string: "+"
      at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
      at java.lang.Integer.parseInt(Integer.java:484)
      at java.lang.Integer.parseInt(Integer.java:527)
      at org.broad.tribble.readers.TabixReader.getIntv(TabixReader.java:274)
      at org.broad.tribble.readers.TabixReader.access$300(TabixReader.java:43)
      at org.broad.tribble.readers.TabixReader$Iterator.next(TabixReader.java:351)
      at org.broad.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:43)
      at com.affymetrix.genometryImpl.symloader.BED$2.next(BED.java:255)
      at com.affymetrix.genometryImpl.symloader.BED$2.next(BED.java:244)
      at com.affymetrix.genometryImpl.symloader.BED.parse(BED.java:211)
      at com.affymetrix.genometryImpl.symloader.BED.processLines(BED.java:269)
      at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLoaderTabix.java:156)
      at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:276)
      at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:154)
      at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:130)
      at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:110)
      at com.affymetrix.genometryImpl.quickload.QuickloadServerType.loadFeatures(QuickloadServerType.java:354)
      at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:955)
      at com.affymetrix.igb.view.load.GeneralLoadUtils$3.loadOnSequence(GeneralLoadUtils.java:859)
      at com.affymetrix.igb.view.load.GeneralLoadUtils$3.access$400(GeneralLoadUtils.java:724)
      at com.affymetrix.igb.view.load.GeneralLoadUtils$3$3.run(GeneralLoadUtils.java:800)
      at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
      at java.util.concurrent.FutureTask.run(FutureTask.java:262)
      at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
      at java.lang.Thread.run(Thread.java:744)

      SUPPLEMENTAL: Seems you can get different outcomes depending on timing of opening the BED file.

      If you open the bed file IMMEDIATELY after opening Blueberry IGB forgets that it was looking at Blueberry and opens the BED file as a custom genome.
      If you open the bed file AFTER TRACKS have been drawn you get the described errors reported in this current jira issue
      If you open the bed file dialog IMMEDIATELY after opening Blueberry but wait for tracks to be loaded you get both outcomes (IGB opens file as custom genome and throws NumberFormat exceptions)

        Attachments

          Activity

          kyle Kyle Suttlemyre (Inactive) created issue -
          ann.loraine Ann Loraine made changes -
          Field Original Value New Value
          Project IGB 8.1 [ 10640 ] IGB 8.2 [ 10840 ]
          Key IGBE-155 IGBF-36
          dcnorris David Norris (Inactive) made changes -
          Assignee Ann Loraine [ aloraine ] David Norris [ dcnorris ]
          dcnorris David Norris (Inactive) made changes -
          Story Points 2
          dcnorris David Norris (Inactive) made changes -
          Rank Ranked higher
          dcnorris David Norris (Inactive) made changes -
          Workflow classic default workflow [ 14383 ] Loraine Lab Workflow [ 14612 ]
          ann.loraine Ann Loraine made changes -
          Rank Ranked lower
          ann.loraine Ann Loraine made changes -
          Rank Ranked higher
          ann.loraine Ann Loraine made changes -
          Rank Ranked higher
          dcnorris David Norris (Inactive) made changes -
          Sprint Sprint 3 [ 6 ]
          dcnorris David Norris (Inactive) made changes -
          Rank Ranked higher
          ann.loraine Ann Loraine made changes -
          Sprint Sprint 3 [ 6 ]
          ann.loraine Ann Loraine made changes -
          Rank Ranked lower
          mason Mason Meyer (Inactive) made changes -
          Epic Link IGBF-497 [ 15559 ]
          mason Mason Meyer (Inactive) made changes -
          Rank Ranked higher
          mason Mason Meyer (Inactive) made changes -
          Rank Ranked lower
          mason Mason Meyer (Inactive) made changes -
          Project IGB [ 10840 ] Deep Backlog [ 11041 ]
          Key IGBF-36 DB-145
          Workflow Loraine Lab Workflow [ 14612 ] jira [ 16852 ]

            People

            • Assignee:
              dcnorris David Norris (Inactive)
              Reporter:
              kyle Kyle Suttlemyre (Inactive)
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              Dates

              • Created:
                Updated: