Please see my current progress and notes regarding this issue:

https://bitbucket.org/pbadzuh/igb_pbdev/branch/IGBF-1443#diff

• The changes I have made create a new track operation UI element and configure it for use in the code.
• The new operation can be seen by opening a bam file in IGB (requires that a respective bai file be present in the same directory), right-clicking on the BAM track title (on the left) -> Track Operations -> Depth Graph (Soft-clip All).
• Todo: Update the collectSoftclipSpans method in the getSymmetrySoftclipSummary method (SoftClipDepthOperator.java) such that only the spans of soft-clip portions of aligned reads are extracted.
• Step through the collectStartSpans and collectLeafSpans methods using the netbeans debugger to understand the data structures and methods being used. This is where I stopped; the output of these methods seemed to be the same with the test files I used, however, this doesn’t seem to be correct. I was not able to identify what exactly constitutes a ‘start span’, so that my be a good start.
• The getSpanSummary function called afterward in getSymmetrySoftclipSummary should generate a depth graph for the entire portions of the isolated soft-clip spans of aligned reads. Should be kept as is.
• I have attached the files I used for testing. Additional files that may be useful in testing can be found here.

Important files:
DepthOperator.java
SeqSymSummarizer.java
SeqUtils.java
BAMSym.java

Implemented Soft Clip and attaching a screenshot for reference.

Please review my changes on this link
https://bitbucket.org/supreeth27/integrated-genome-browser/commits/9c50e7d7dcbafdecbed40cfcfc781f1adb67200d
These changes are done by Philip Badzuh
https://bitbucket.org/supreeth27/integrated-genome-browser/commits/9921fba899dc022b5df80aee051bafe8307fb6c9

I have reviewed the code and made a few comments. I am not recommending any changes, apart from possibly adding more comments to the new method in SeqUtils. But this is completely optional – if you think the current documentation along with the commit history is enough to guide future developers, then that is fine with me! As you have recently done a deep dive into this part of the code, your judgement is best.

I have not done a functional review. Nowlan Freese - would you do a functional review when you get the chance? Also please check the code for possible "gotchas" we may not have considered.

Sai Supreeth Segu are all of the changes (including Philips) pushed to your branch?

Nowlan Freese All the changes(including Philips) are on my branch.
Link to my branch: https://bitbucket.org/supreeth27/integrated-genome-browser/src/IGBF-1443/

Tested Supreeth's branch on Mac with files from GIAB and the test softclip files in Dropbox.

Depth Graph (Soft-clip All) works correctly for all tested BAM/SAM files.
Depth Graph (Soft-clip All) option only shows for BAM/SAM files (this is the correct behavior, as only BAM/SAM will have softclips).

Code is similar to existing depth graph all code, but is separate so should not interfere.

Recommend pull request Sai Supreeth Segu.

Created pull request.
Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/826/igbf-1443

[~aloraine] if you could please review the pull request.

Merged. Master branch installers are available and ready for testing.

Tested master dmg installer for Mac.

Depth Graph (Soft-clip All) working correctly.

Closing issue.