Details
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Type:
Improvement
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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: 8.5.0 Major Release
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Labels:
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Story Points:0.5
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Epic Link:
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Sprint:Sprint 29
Description
Cloud storage providers like Dropbox typically make it possible for users to create links to files and then share the links. However, paths exposed in links don't correspond to physical storage, which means that IGB can't make assumptions about the location of index files for BAM, tabix, or other indexed, random access formats.
Let's add a new optional attribute ("index") to the QuickLoad "file" tag where "index" indicates the location of the index file. Same rules about defining file locations should apply.
Attachments
Issue Links
- relates to
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REL-15 Create example BAM/BAI Quickloads
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- Testing Complete
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Activity
Testing for this issue included:
-Verifying that annots.xml files with an index tag use the index in the specified location (verified on Mac and Windows).
-Verifying that the index file specified in the index tag overrides any index file in the folder with the file needing indexing.
-I removed the index attribute for bam files to verify that the bam would not load.
-I tested loading of bam files with an index file in the same directory and with an index file specified in the annots.xml to test differences and see which one gets used if both are present (annots.xml overrides an index in same directory).
While testing I noticed that the index attribute in the annots.xml file is being ignored for local Quickloads.
We should look into this to see if this can be fixed for local Quickloads.
Reassigning to John to take a look at this issue.
Yes, we definitely will want to fix this, as people might think they can put indexes in other places besides the same directory as the target (indexed) file.
Testing for this issue included:
-Verifying that annots.xml files with an index tag use the index in the specified location (verified on Mac and Windows).
-Verifying that the index file specified in the index tag overrides any index file in the folder with the file needing indexing.
-I removed the index attribute for bam files to verify that the bam would not load.
-I tested loading of bam files with an index file in the same directory and with an index file specified in the annots.xml to test differences and see which one gets used if both are present (annots.xml overrides an index in same directory).
-Verifying that the index attribute in the annots.xml for local Quickloads is not being ignored.
Since this story is resolved it will now be closed.
This comment sounds wrong:
"I removed the index attribute for bam files to verify that the bam would not load."
If you remove the index attribute, then the file should STILL load if the index is in the same directory as the BAM file.
The index attribute is optional, not required. If the index file attribute is not present in the annots.xml file, then IGB should attempt to retrieve the index file from the same directory (context root) where the BAM file is located.
http://test.bioviz.org/quickload/