See: https://bitbucket.org/lorainelab/softclip_track_operation/src/master/

The issue occurs in the SeqUtils.java file in the collectSoftclipSpans method. The general idea for the method is to recursively move through a sym finding its children. If that child is a BAM sym and it has softclipping children then the softclipping children's spans are added to the leafs. However, the issue arises that a bamsym can have many repeating children, each of which has a copy of the softclipping children.

To fix the issue, after a BAMSym is found and following the loop for(int ii = 0; ii < bamSym.getSoftChildCount(); ii++){ we can add either a break or set the ii variable to bamSym.getSoftChildCount() to prevent the loop from continuing through all of the repeating children.

The reason this occurs seems to have to do with how BAM syms are now separated. If a matching part of a BAM sym has an insertion located in the middle, the matching part before the insertion is considered one child, the insertion another child, and the final matching part the 3rd child.

Next steps: Revert soft clip graph feature and implement fix in App - https://bitbucket.org/lorainelab/softclip_track_operation/src/master/

Commits to revert:

• https://bitbucket.org/lorainelab/integrated-genome-browser/commits/aeb1873cb8c2239c219ab739dbd4e9dcdbbebc6a IGBF-1443 : Adding comments for new methods
• https://bitbucket.org/lorainelab/integrated-genome-browser/commits/9c50e7d7dcbafdecbed40cfcfc781f1adb67200d IGBF-1443 : Implement Depth Graph(Soft-clip)
• https://bitbucket.org/lorainelab/integrated-genome-browser/commits/9921fba899dc022b5df80aee051bafe8307fb6c9 IGBF-1443: Add skeleton for the implementation of depth graph for soft-clip portions of aligned reads

Reverted commits. Built on my local. Soft-clip depth graph option now absent.
Branch: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-2647?dest=master

Nowlan Freese and Sai Supreeth Segu - please review PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/851/igbf-2647

Main thing is to make sure all original changes are removed. (Recall that we are now implementing this as an App instead of a change to the IGB platform code base.)

[~aloraine] Yes, all the original changes are removed. Please, go ahead and merge the pull request.

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.