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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- Closed
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Activity
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:
samtools view -b Malintka-R1-0hr-25C-self.bam SL4.0ch10:64782127-64792705 > SL40ch10_64782127_64792705.bam samtools index SL40ch10_64782127_64792705.bam
To test the SL40ch10_64782127_64792705.bam with find junctions run:
java -jar find-junctions-1.0.0-jar-with-dependencies.jar -u -f 5 -b S_lycopersicum_Sep_2019.2bit -o SL40ch10_64782127_64792705.FJ.bed SL40ch10_64782127_64792705.bam
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.
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)