Error encountered querying alignments: java.lang.NullPointerException

nk

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Jun 19, 2015, 11:15:43 AM6/19/15

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I get the above error message for every BAM file that I try to load in IGV. Using version 2.3.56 on Java 8.

Log:

ERROR [2015-06-19 16:11:20,618] [AlignmentTileLoader.java:239] [pool-2-thread-4] Error loading alignment data
java.lang.NullPointerException
    at org.broad.igv.sam.SpliceJunctionHelper.addAlignment(SpliceJunctionHelper.java:117)
    at org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:380)
    at org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:175)
    at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:327)
    at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:292)
    at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:57)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
INFO [2015-06-19 16:11:20,622] [MessageUtils.java:60] [pool-2-thread-4] <html>Error encountered querying alignments: java.lang.NullPointerException

Any ideas what this might be? I don't think it's file corruption since I have previously loaded this file in IGV (and the error also occurs for other files).

Thanks

Jim Robinson

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Jun 19, 2015, 12:06:38 PM6/19/15

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Hi,

Could you attach your "prefs.properties" file, located in the IGV folder?

Jim

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nk

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Jun 19, 2015, 12:09:21 PM6/19/15

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Sure, here it is.

Cheers

prefs.properties

Jim Robinson

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Jun 19, 2015, 12:39:28 PM6/19/15

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Thanks, it looks like this has been a latent bug waiting to happen for some time, I'm still not sure why your particular mix of preferences triggered it but I have put a "null check" around the offending code that should fix it. The fix is building now, it will be version 2.3.57.

Jim

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nk

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Jun 19, 2015, 1:53:52 PM6/19/15

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Perfect, that seems to have done the trick.

Thank you!

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