Details
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Type:
Bug
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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:2
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Epic Link:
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Sprint:Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 4 2021 May 3 - May 14
Description
Situation: The Depth Graph (Soft-clip All) track operation on PacBio data is providing incorrect results.
To replicate:
Load the H_sapiens_Dec_2013 genome.
Add the attached sonAshMinimap2_1LINE.bam file.
Navigate to chr1:10,643,151-10,643,319
Click load data.
Right-click on the bam file track label and select Track Operations > Depth Graph (Soft-clip All).
Note that there is one soft clip at the beginning of the read, but the graph states there are approximately 800 soft clips.
Task: Fix the Depth Graph (Soft-clip All) operator so that it displays the correct soft-clip depth information for PacBio files.
Attachments
Issue Links
Activity
Changes are merged & new master branch installers are built. See: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/
Nowlan Freese - please confirm that the functionality is correctly implemented. Please check that latest released version of IGB - version 9.1.6 - can install the new soft clip App. To get the soft-clip app, please use this repository: https://bitbucket.org/lorainelab/softclip_track_operation/downloads/
Tested on Mac release 9.1.6
Can install app "Graph Soft Clips" from https://bitbucket.org/lorainelab/softclip_track_operation/downloads/
App adds "Added App - Graph Soft-Clips" as a right-click track operation.
Issues:
1) Need to rename the right-click track operation to something like "Depth Graph (Soft-clip All)"
2) Changes to fix the soft-clip depth operator do not appear to have been added to the app.
Currently working on the softclip track operatior app in IGB 9.1.8
I have updated the right-click track operation's name to read Depth Graph (Soft-clip all) as Dr. Freese suggested above.
My main point of focus in tackling this issue stems mainly within SoftClipDepthOperator.java and SoftClipUtils.java as I work through the logic to tackle the main issue in why the soft clip operator has not changed.
I have attached screenshots of what happens from before/after the depth graph is selected.
My main question is what exactly should the soft-clip depth operator show for a correct operation in this case? A graph Y-value of 800 for the whole track or just the first three entries of the sequence?
Observations 3/25 -
Using a break to escape the for loop doesn't seem to do anything, in the case of the new files. Instead of giving the correct value of 4, each x value is 12. In addition, I added a potential change to the ii variable, setting it equal to the number of soft clips, I will continue testing
Observations 3/30 -
Because the for loop where the problems seems to be is within another for loop, I noticed that putting a break outside of the first one (so that only one instance of the parent for loop would execute) would cause none of the Soft Clip entries to show up on the graph.
The main method also seems to be somewhat recursive so the reason it is looping in on itself multiple times may have to do with this implementation as well.
For the attached file sonAshMinimap2_1LINE.bam the correct depth operator should show a value of 1.
See: https://bitbucket.org/lorainelab/softclip_track_operation/src/master/