Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
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Environment:
Windows v9908
Description
1. Open IGB
2. No species loaded
3. Drag and drop in local .CHP file (attached)
Throws error in console:
MainWorkspaceManager:itemStateChanged hit
MainWorkspaceManager:itemStateChanged hit
Jan 23, 2012 1:24:05 PM com.affymetrix.igb.featureloader.QuickLoad logException
WARNING: BGZF file has invalid uncompressedLength: -216092498
java.lang.RuntimeException: BGZF file has invalid uncompressedLength: -216092498
at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:376)
at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361)
at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109)
at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234)
at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:159)
at com.affymetrix.genometryImpl.util.GeneralUtils.unzipFile(GeneralUtils.java:451)
at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:602)
at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:589)
at com.affymetrix.igb.featureloader.QuickLoad.getGenome(QuickLoad.java:379)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddAllSymmetries(QuickLoad.java:273)
at com.affymetrix.igb.featureloader.QuickLoad.access$000(QuickLoad.java:46)
at com.affymetrix.igb.featureloader.QuickLoad$1.runInBackground(QuickLoad.java:194)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NegativeArraySizeException
at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:374)
... 19 more
Jan 23, 2012 1:24:05 PM com.affymetrix.igb.featureloader.QuickLoad logException
WARNING: null
java.lang.NullPointerException
at com.affymetrix.igb.featureloader.QuickLoad.addMethodsToFeature(QuickLoad.java:306)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddAllSymmetries(QuickLoad.java:286)
at com.affymetrix.igb.featureloader.QuickLoad.access$000(QuickLoad.java:46)
at com.affymetrix.igb.featureloader.QuickLoad$1.runInBackground(QuickLoad.java:194)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
MainWorkspaceManager:itemStateChanged hit
MainWorkspaceManager:itemStateChanged hit
Attachments
Issue Links
- relates to
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BUG-622 File format issues
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- Closed
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1. |
CHP legacy format file don't show up in table |
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Closed | Unassigned |