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.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3251 [ 22132 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Molly Davis [ molly ] |
| Attachment | Junction_Error.png [ 17954 ] | |
| Attachment | SL4_ch10.png [ 17955 ] |
| Attachment | SL40ch10_64782127_64792705.bam [ 17956 ] | |
| Attachment | SL40ch10_64782127_64792705.bam.bai [ 17957 ] |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |