-
Notifications
You must be signed in to change notification settings - Fork 3
Closed
Milestone
Description
When the user provides a file with two barcodes (or more) and use the default value for the barcode tag (BC), it throws with an uninformative error: UNEXPECTED ERROR: 1. This is an index out of bound exception, and it should be checked and/or cached.
After running with debug, this is the error and the stacktrace:
***********************************************************************
UNEXPECTED ERROR: 1
***********************************************************************
Please, search for this error in our issue tracker or post a new one:
https://github.com/magicDGS/ReadTools/issues
java.lang.ArrayIndexOutOfBoundsException: 1
at org.magicdgs.readtools.tools.barcodes.dictionary.decoder.BarcodeDecoder.lambda$getBestBarcodeString$6(BarcodeDecoder.java:218)
at java.util.stream.IntPipeline$4$1.accept(IntPipeline.java:250)
at java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:110)
at java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:693)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.magicdgs.readtools.tools.barcodes.dictionary.decoder.BarcodeDecoder.getBestBarcodeString(BarcodeDecoder.java:222)
at org.magicdgs.readtools.tools.barcodes.dictionary.decoder.BarcodeDecoder.assignReadGroupByBarcode(BarcodeDecoder.java:181)
at org.magicdgs.readtools.tools.barcodes.AssignReadGroupByBarcode.apply(AssignReadGroupByBarcode.java:166)
at org.magicdgs.readtools.engine.ReadToolsWalker.lambda$new$52(ReadToolsWalker.java:147)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at org.magicdgs.readtools.engine.ReadToolsWalker.traverse(ReadToolsWalker.java:131)
at org.magicdgs.readtools.engine.ReadToolsWalker.doWork(ReadToolsWalker.java:194)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:116)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:121)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:142)
at org.magicdgs.readtools.Main.main(Main.java:84)
Action here requires:
- Add a FAQ entry asap to inform about this error
- Catch this error and throw an user exception which is informative
Reactions are currently unavailable
Metadata
Metadata
Assignees
Labels
No labels