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: 9.1.10 Major Release
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15
Description
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See:
core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java
Note that "Runtime" lines are incompatible with Java 18. See this commit for invocation of Runtime obsolete stack trace setting method.
Attachments
Issue Links
- relates to
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IGBF-3705 Add USEQ support back to IGB
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- Closed
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Testing master branch installer on Mac OS 12.5
Reset preferences to default and delete the .igb folder.
Attempting to load the attached useq file into the H_sapiens_Mar_2006 genome resulted in a "Format not recognized" error. This is the appropriate behavior.
In the A_thaliana_Jun_2009 genome, loaded the RNA-Seq > Auxin arf19 > Graph - Scaled > Col-0 control scaled coverage graph file successfully.
Closing ticket.