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: 9.1.10 Major Release
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Labels:None
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Story Points:4
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Epic Link:
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Sprint:Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14
Description
Situation: bigBed is an indexed binary format of bed files. However, in IGB, bigBed files are not appearing correctly. The bigBed gene annotations (see attached file) are not showing the introns/exons, but instead are drawing a single glyph for the entire gene.
Task: Fix IGB so that the bigBed files appear correctly.
See the UCSC guide on bigBed for more information on the bigBed file format.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Attachment | bbVSbed.png [ 16793 ] |
| Attachment | Araport11.bb [ 16794 ] |
| Attachment | bedDetail.as [ 16795 ] |
| Description |
Situation: bigBed is an indexed binary format of bed files. However, in IGB, bigBed files are not appearing correctly. The bigBed gene annotations (see attached file) are not showing the introns/exons, but instead are drawing a single glyph for the entire gene.
Task: Fix IGB so that the bigBed files appear correctly. See the [UCSC guide on bigBed|] for more information on the bigBed file format. |
Situation: bigBed is an indexed binary format of bed files. However, in IGB, bigBed files are not appearing correctly. The bigBed gene annotations (see attached file) are not showing the introns/exons, but instead are drawing a single glyph for the entire gene.
Task: Fix IGB so that the bigBed files appear correctly. See the [UCSC guide on bigBed|https://genome.ucsc.edu/goldenPath/help/bigBed.html] for more information on the bigBed file format. |
| Assignee | Nowlan Freese [ nfreese ] |
| Sprint | Fall 6 2021 Oct 25 - Nov 5 [ 132 ] | Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 19 [ 132, 133 ] |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Sprint | Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24 [ 132, 133 ] | Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10 [ 132, 133, 134 ] |
| Rank | Ranked higher |
| Sprint | Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10 [ 132, 133, 134 ] | Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24 [ 132, 133, 134, 135 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Story Points | 3 | 4 |
| Summary | Fix bigBed parsing | Improve bigBed parsing |
| Assignee | Nowlan Freese [ nfreese ] | Omkar Marne [ omarne ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Attachment | bed.png [ 17045 ] |
| Attachment | bed and bb.png [ 17046 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Omkar Marne [ omarne ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24 [ 132, 133, 134, 135 ] | Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14 [ 132, 133, 134, 135, 136 ] |
| Rank | Ranked higher |
| Attachment | chrom.sizes [ 17047 ] |
| Assignee | Omkar Marne [ omarne ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Omkar Marne [ omarne ] | Nowlan Freese [ nfreese ] |
| Fix Version/s | 9.1.10 Major Release [ 10700 ] |