Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Major
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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:
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Story Points:10
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Sprint:B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3, Fall 2018 Sprint 4
Description
IGB should show soft-clipped bases in BAM files.
Attachments
Issue Links
- relates to
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IGBF-1440 Fix soft-clipping glyph render
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- Closed
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- Closed
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IGBF-1443 Implement Depth Graph (Soft-clip)
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- Closed
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- Closed
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- Closed
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- To-Do
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IGBF-1222 Check if IGB shows soft-clipped bases from read alignments correctly
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- Closed
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Activity
| Attachment | soft.png [ 14102 ] |
| Attachment | soft.png [ 14102 ] |
| Attachment | softclip_igv.png [ 14103 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018 [ 48 ] | B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ] |
| Rank | Ranked higher |
| Attachment | SoftClipped.png [ 14116 ] |
| Labels | Advanced |
| Summary | Correct how IGB shows soft-clipped bases in BAM files | Allow showing soft-clipped bases in BAM files |
| Summary | Allow showing soft-clipped bases in BAM files | Show soft-clipped bases in BAM files |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
Adding David's comments here for future reference:
Initial thoughts:
1. You need to store everything you need to dynamically visualize the read in the data model when the file is loading.
2. My understanding is likely very poor at this stage, but this probably means creating a custom "Sym" type that cares for the details of rendering.
Additional quick thought that may or may not be useful:
It seems the start position of the sym/glph is impacted by the soft clipping toggle. I think instead of hard-coding the position of the BAMSym at parse time you could instead capture fields in BamSym like softClipStartPosition and defaultStartPosition and then dynamically return one or the other depending on the preferences based toggle.
i.e. in the getter for this property you could have an if condition that references this global preferences boolean
boundaries of the glyph are important in steps such as packing, so I think you will need to take special care to repack/refresh the view when this toggle is triggered and the data model is parsed again for rendering.
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3 [ 48, 49, 50 ] |
| Rank | Ranked higher |
| Story Points | 2 | 10 |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Assignee | Kiran Korey [ kkorey ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Anh Moss [ aduong ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3 [ 48, 49, 50 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 48, 49, 50, 51 ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 48, 49, 50, 51 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2 [ 48, 49, 50, 51, 52 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2 [ 48, 49, 50, 51, 52 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3 [ 48, 49, 50, 51, 52, 53 ] |
| Assignee | Anh Moss [ aduong ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Nowlan Freese [ nfreese ] |
I am going to try to implement soft-clipping visualization similar to how insertions are drawn.
This will most likely involve editing the following files:
- BAMSym.java
- XAM.java
- BAM.java
- SAM.java
- AnnotationGlyphFactory.java
When testing, it will be important to look at memory use, as we will be drawing new glyphs for each instance of soft-clipping.
We will also need to check paired-end reads, as they add an additional layer of complexity.
My current branch with implemented softclipping:
https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-1291-Softclipping
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Needs 1st Level Review [ 10005 ] |
New implementation showing soft clips as black rectangles with red triangles. The soft clip glyph shows up on the first/last nucleotide that is matched (M on cigar string) after/before the soft clip.
| Attachment | softClipExample.png [ 14156 ] |
| Attachment | Leaf1.small.aligned.sorted.softClipped.bam [ 14157 ] | |
| Attachment | Leaf1.small.aligned.sorted.softClipped.bam.bai [ 14158 ] |
| Status | Needs 1st Level Review [ 10005 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] |
New implementation shows the entire length of the soft clip. Soft clip is selectable and has tooltips and edge matching.
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3 [ 48, 49, 50, 51, 52, 53 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3, Fall 2018 Sprint 4 [ 48, 49, 50, 51, 52, 53, 54 ] |
| Rank | Ranked higher |
New implementation has more options, better selection through menu. Appears to be working with the changes to HTSJDK.
| Status | In Progress [ 3 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Needs Testing [ 10002 ] |
| Rank | Ranked higher |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
Tested using master branch of Loraine Lab and also using local build on Windows.
The functionality is working correctly and the menu options are also easy to understand now. The code is not breaking anywhere.
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 9.0.2 Minor Release [ 10600 ] |
| Fix Version/s | 9.1.0 Major Release [ 10601 ] |
| Link | This issue relates to IGBF-9 [ IGBF-9 ] |
| Workflow | Loraine Lab Workflow [ 17982 ] | Fall 2019 Workflow Update [ 19881 ] |
| Workflow | Fall 2019 Workflow Update [ 19881 ] | Revised Fall 2019 Workflow Update [ 22000 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] | Nowlan Freese [ nfreese ] |
Enable IGB users to show or hide soft-clipped bases in BAM tracks.
Add option to track label context menu - "Show soft-clipped bases"
See image for wording and placement relative to other menu items.