Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Minor
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.1.0 Major Release
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Labels:None
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Story Points:2
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Sprint:Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3, Spring 2019 Sprint 1
Description
Depth graph track operations are used to add up the amount of read depth from bam/sam files. The soft-clipped portion of a read should not count towards either Depth Graph (Start) or Depth Graph (All).
Currently Depth Graph (All) does not include the soft-clipped portion (correct). However, Depth Graph (Start) does count the soft-clipped portion (bug).
Example soft-clip files can be found in Dropbox > IGB > Jira Issues > IGBF-1291 Soft-Clip > exampleFiles
Potential classes worth investigating:
SeqSymSummarizer > getSpanStartSummary
Delegate - getRegion
Attachments
Issue Links
- relates to
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IGBF-1291 Show soft-clipped bases in BAM files
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- Closed
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Activity
From what we can tell, the StartDepthOperator is only used by the track operation > Depth Graph (Start). The edits made to StartDepthOperator do not seem to affect other track operations, however, a more thorough examination/testing may be needed.
We need to consider how this will work with bed files. Bed files will have multiple sym leafs, and each will have its own start. This is also an issue with BAM files where the matching section is split by a deletion, creating two leafs.
Updated the logic. Please review
https://bitbucket.org/ptambvekar/igb-pranav-fork/commits/branch/IGBF-1441-fix-depth-graph-soft-clip
Dr. Loraine pointed out that GFF files do not have to be positionally sorted. Thus, the first index position of the sym object does not necessarily contain the beginning of the annotation for GFF files. We need to identify the child sym with the correct start before adding it as a leaf.
Expect to spend probably 2 full days on this.
Link to dropbox folder with files: https://www.dropbox.com/sh/wxzhideujatu6ct/AAB3OafXzmTAXuu3eZTGYcGBa?dl=0
Explanation of CIGAR string: http://bioinformatics.cvr.ac.uk/blog/tag/cigar-string/
Working:
1. Depth Graph (Start) for not considering soft-clip works fine for Bam and Sam files on https://www.dropbox.com/sh/wxzhideujatu6ct/AAA4s1PZVa9JjYkN4Bpi1rHba/exampleFiles?dl=0&subfolder_nav_tracking=1, also for attached bam,sam files
2. Behavior for All the file format available in Smoke Test data at (http://igbquickload.org/smokeTestingQuickload/) except for GFF3 is in sync with Relase 9.0.2
Not Working:
1. Please refer attached 'IGBF1441_Testing' document for failure test case details. Depth Graph(Start) for GFF3 files are not generating any graphs. This can be checked against IGB with Release 9.0.2 . (Data Used is smoke testing data as mentioned in point 2 above)
Need testing on my current branch to see if the GFF3 files are now working correctly.
Please Check 'IGBF1441_Review_Screenshot' attached file.
Downloaded installer from https://bitbucket.org/nfreese/nowlanfork-igb/downloads/ with name 'IGB-IGBF-1441-SoftclipDepthGraphStartBug-x64.exe' and it is now showing Depth Graph(Start) for GFF3 files loaded from smoking test data
Testing Mac: Working Correctly
Linux testing successful
Testing Windows: Working Correctly
Made changes at the branch:
https://bitbucket.org/ptambvekar/igb-pranav-fork/src/IGBF-1441-fix-depth-graph-soft-clip/