Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Fall 1 - Sep 5
Description
Relates to error: IGBF-3420
Error:
Exception in thread "main" java.lang.RuntimeException: Postion is too high (more than 64792705)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.setCurrentSequencePosition(TwoBitParser.java:191)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.loadFragment(TwoBitParser.java:332)
at org.lorainelab.findjunctions.FindJunctions.main(FindJunctions.java:249)
Issue: Looked at the bam file which looks fine but there are reads that expand upon the chromosome. They have been soft clipped but find_junctions isn't taking that into consideration and won't process the file entirely to create the .FJ.bed.gz file.
Visualize the error in IGB.
