Details
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Type:
Task
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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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:4
Description
Situation: When running the FindJunctions program, if a read runs past the end of the specified chromosome length an error is thrown that stops the processing of the rest of the file.
Task: Modify the FindJunctions program so that if a "Position is too high" error is thrown it is caught and reported and then the program continues to proceed instead of exiting.
FindJunctions repository: https://bitbucket.org/lorainelab/findjunctions/src/master/
Attachments
Issue Links
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Activity
The error that is thrown:
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)
I have added a test bam file with the problematic reads (SL40ch10_64782127_64792705.bam as well as its index) from Malintka-R1-0hr-25C-self.bam.
Code:
To test the SL40ch10_64782127_64792705.bam with find junctions run:
The S_lycopersicum_Sep_2019.2bit file can be found here.
The find-junctions-1.0.0-jar-with-dependencies.jar can be found here.