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  1. IGB
  2. IGBF-522

Saving a track as a Bed-detail file generates an exception

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          An exception is generated when using IGB's "Save Track As..." feature.

          To reproduce:
          1) Open the A. thaliana genome and use the "Save Track As..." option in the context menu to save a "bed-detail" file. (Must change drop-down box for file type)

          *Observe:
          An exception is generated:

          15:28:40.285 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedSym.outputBedFormat(UcscBedSym.java:229) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.289 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.291 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedSym.outputBedFormat(UcscBedSym.java:268) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.295 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedSym.outputBedFormat(UcscBedSym.java:269) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.296 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:59) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.298 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedSym.outputBedFormat(UcscBedSym.java:227) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.299 ERROR c.a.genometry.util.GeneralUtils - null
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.util.GeneralUtils.safeClose(GeneralUtils.java:72) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:119) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          ... 43 common frames omitted

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              mason Mason Meyer (Inactive) added a comment -

              My testing verifies that this issue has been resolved so it will now be closed.

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              mason Mason Meyer (Inactive) added a comment - My testing verifies that this issue has been resolved so it will now be closed.
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              dcnorris David Norris (Inactive) added a comment -

              fixed

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              dcnorris David Norris (Inactive) added a comment - fixed

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                • Assignee:
                  dcnorris David Norris (Inactive)
                  Reporter:
                  mason Mason Meyer (Inactive)
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                  • Created:
                    Updated:
                    Resolved: