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 9
Description
Situation: When copying a BAM track the copied track is missing several Track Operations options, including Find Junctions.
Task: Investigate why Track Operations > Find Junctions is missing from a copied BAM track.
To reproduce:
- Open the hg38 human genome (H_sapiens_Dec_2013)
- Go to chr16:28,931,601-28,939,711
- Select File > Open URL...
- Paste the following URL and click OK - https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/H_sapiens_Dec_2013/Bam/BAM_hg38_10k_PBMC_CD19.bam
- Click Load Data
- Right-click on the track label and select Track Operations > Copy
- A new track should be created that is a copy of the original track
- Click Load Data
- Right-click on the track label of the new Copy track and select Track Operations - Note that Find Junctions and Find Junctions (TopHat) are missing.
Attachments
Activity
PR is merged. Installers built and deployed to bioviz.org. Ready for testing.
Tested with Dr. Freese, FindJunctions is now able to be used on copied BAM tracks. No errors in the Log.
Recommending PR!
Branch code changes: https://bitbucket.org/lorainelab-deepthi/integrated-genome-browser/branch/IGBF-4373
Created CopyAlignmentOperator.operate() to preserve the original track's ext when creating the copy. It uses reflection to read the private ext from the source TypeContainerAnnot (defaulting to "bam" if unavailable), then creates the copy with new TypeContainerAnnot(t.getType(), ext, false) instead of new TypeContainerAnnot(t.getType()) used CopyXOperator.java file as reference. This ensures the copied track maintains FileTypeCategory.Alignment instead of defaulting to Annotation, so alignment-specific operations like "Find Junctions" remain available in the Track Operations menu.
FindJunctions is now an option for both BAM and copied BAM tracks. Creating multiple copied tracks and multiple FindJunctions tracks does not cause any issues. I can apply filters and other settings to these tracks as expected. No errors in the Log.
At one point, I ran into an issue during testing where the Lock/Unlock Track Height option was greyed out incorrectly but I am unable to reproduce this issue and I'm not sure what originally called it.
Closing this ticket!