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
| Attachment | softClipShifted2.sam [ 14173 ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Attachment | onlyMatchesNegativeShifted.sam [ 14177 ] | |
| Attachment | onlyMatchesShifted-2.sam [ 14178 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
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.
| Status | Pull Request Submitted [ 10101 ] | Reviewing [ 10301 ] |
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.
| Attachment | example.bed [ 14182 ] | |
| Attachment | soft-match-deletion-match-insertion-match-soft.sam [ 14183 ] |
| Attachment | VCF_HomoSapien_EDITED.vcf [ 14184 ] |
Updated the logic. Please review
https://bitbucket.org/ptambvekar/igb-pranav-fork/commits/branch/IGBF-1441-fix-depth-graph-soft-clip
| Status | Reviewing [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Nowlan Freese [ nfreese ] | Pranav Sanjay Tambvekar [ ptambvek ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing [ 10301 ] |
| Attachment | GFF3_example_1_EDITED.gff3 [ 14185 ] |
| Attachment | GFF3_example_1_EDITED_negative.gff3 [ 14186 ] |
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.
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 4 [ 54 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5 [ 54, 55 ] |
| Rank | Ranked higher |
| Fix Version/s | 9.1.0 Major Release [ 10601 ] |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 4, Fall 2018 Sprint 5 [ 54, 55 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1 [ 54, 55, 56 ] |
| Rank | Ranked higher |
| Status | Reviewing [ 10301 ] | Needs Testing [ 10002 ] |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1 [ 54, 55, 56 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 54, 55, 56, 57 ] |
Expect to spend probably 2 full days on this.
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] | Srishtee Marotkar [ srishtee ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
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)
| Attachment | IGBF1441_Testing.docx [ 14202 ] |
| Comment | [ Details for Failed Test Cases ] |
| Status | Testing In Progress [ 10003 ] | Open [ 1 ] |
| Assignee | Srishtee Marotkar [ srishtee ] |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 54, 55, 56, 57 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3 [ 54, 55, 56, 57, 58 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Need testing on my current branch to see if the GFF3 files are now working correctly.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Srishtee Marotkar [ srishteem ] |
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
| Attachment | IGBF1441_Review_Screenshot.PNG [ 14204 ] |
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Srishtee Marotkar [ srishteem ] | Nowlan Freese [ nfreese ] |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3 [ 54, 55, 56, 57, 58 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 54, 55, 56, 57, 58, 59 ] |
| Rank | Ranked higher |
| Assignee | Nowlan Freese [ nfreese ] | Kiran Korey [ kkorey ] |
| Assignee | Kiran Korey [ kkorey ] | Nowlan Freese [ nfreese ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Attachment | softClip-DepthGraphStart-CORRECT.png [ 14241 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | Reviewing Pull Request [ 10303 ] | Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
Testing Mac: Working Correctly
Linux testing successful
Testing Windows: Working Correctly
| Resolution | Done [ 10000 ] | |
| Status | Needs Testing [ 10002 ] | Closed [ 6 ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] | Srishtee Marotkar [ srishteem ] |
| Workflow | Loraine Lab Workflow [ 18147 ] | Fall 2019 Workflow Update [ 19967 ] |
| Workflow | Fall 2019 Workflow Update [ 19967 ] | Revised Fall 2019 Workflow Update [ 22088 ] |
| Assignee | Srishtee Marotkar [ srishteem ] | Nowlan Freese [ nfreese ] |
Made changes at the branch:
https://bitbucket.org/ptambvekar/igb-pranav-fork/src/IGBF-1441-fix-depth-graph-soft-clip/