Details
-
Type:
Bug
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 8.5.2 MInor Release
-
Labels:
-
Story Points:0.25
-
Sprint:Sprint 30
Description
Insertion Glyph bases are not being shown correctly.
The Glyph is black (correct) but the bases are no longer being shown.
To repeat:
1) Visit S. lycopersicum (tomato) genome
2) Select chromosome chrC-NC_007898.3
3) Select a dataset from Plastid Resequencing folder (not Primers or Amplicon - choose one of the others)
4) Zoom in, load data
5) Zoom in further, look for black insertion Glyphs
6) Observe that bases are not being shown.
What should happen is that bases flanking the insertion site should be displayed on top of the black glyph.
Attachments
Issue Links
- is duplicated by
-
-
- Closed
-
Activity
| Attachment | Insertions8_5_1.png [ 13250 ] |
| Attachment | InsertionBasesOffset.png [ 13255 ] |
| Status | Open [ 1 ] | Needs Testing [ 10002 ] |
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Rank | Ranked higher |
Testing for this issue included:
-Verifying that insertions are looking as expected in BAM files as well as VCF files.
-Verifying that Selection Info and tooltips for insertions are displaying proper info.
-Verifying that insertion placement and sequence info is accurate.
-Verifying that BAM and VCF visualization has not been adversely affected by these changes.
| Fix Version/s | 8.5.2 MInor Release [ 10200 ] |
| Assignee | Mason Meyer [ mason ] | Tarun Mall [ tmall ] |
| Assignee | Tarun Mall [ tmall ] | Mason Meyer [ mason ] |
While testing this issue I noticed that VCF insertions only show one base pair letter on the insertion rather than 2 (see screenshot "VCF_Insertion.png").
I am waiting on feedback to determine if this is expected or not, but if it is then this story can be closed since all other aspects of this story have passed testing.
| Attachment | InsertionsFinal.png [ 13258 ] | |
| Attachment | VCF_Insertion.png [ 13259 ] |
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Open [ 1 ] |
| Labels | File_Formats |
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 16921 ] | Fall 2019 Workflow Update [ 19740 ] |
| Workflow | Fall 2019 Workflow Update [ 19740 ] | Revised Fall 2019 Workflow Update [ 21859 ] |
While testing this issue I noticed that the Insertion bases are now being displayed on the black boxes, but I don't think they look as good as they could. The bases are slightly offset so that the left base is kind of bleeding into the nucleotide beside it. Because of this, I am moving it back to the To-Do column and assigning it to David.