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: None
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Labels:
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Story Points:3
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Sprint:Winter 2018 Sprint 3, Spring 2019 Sprint 1
Description
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. The SNP is present in both files, but IGB only finds it in one of the files.
See Dr. Freese for files.
Computer used - Mac. IGB version 8.5.2
Task:
- Determine if you can reproduce the error using files provided by Dr. Freese
- Investigate & report why this error is occurring
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-497 [ 15559 ] |
| Rank | Ranked higher |
| Epic Link | IGBF-497 [ 15559 ] |
| Rank | Ranked higher |
| Description |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. I have only been able to replicate this with the files we used for the outreach event, which were gzipped and tabix indexed. See Nowlan for files. Computer used - Mac. IGB version 8.5.2 |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring * If a fix is obvious & simple, go ahead and do it. |
| Story Points | 1 | |
| Sprint | Winter 2018 Sprint 3 [ 58 ] | |
| Labels | Beginner |
| Description |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring * If a fix is obvious & simple, go ahead and do it. |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. The SNP is present in both files, but IGB only finds it in one of the files. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring * If a fix is obvious & simple, go ahead and do it. |
| Rank | Ranked higher |
| Attachment | mysteryBabyDad.bed.gz [ 14208 ] | |
| Attachment | mysteryBabyMom.bed.gz [ 14209 ] |
| Attachment | mysteryBabyMom.bed.gz [ 14209 ] |
| Attachment | mysteryBabyDad.bed.gz [ 14208 ] |
| Attachment | diseaseDad.bed.gz [ 14219 ] | |
| Attachment | diseaseDad.bed.gz.tbi [ 14220 ] | |
| Attachment | diseaseMom.bed.gz [ 14221 ] | |
| Attachment | diseaseMom.bed.gz.tbi [ 14222 ] |
| Attachment | Screen Shot 2016-02-18 at 5.20.44 PM.png [ 13275 ] |
| Attachment | missingSearch.png [ 14223 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Rank | Ranked higher |
| Sprint | Winter 2018 Sprint 3 [ 58 ] | Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ] |
| Rank | Ranked higher |
| Story Points | 1 | 3 |
| Description |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. The SNP is present in both files, but IGB only finds it in one of the files. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring * If a fix is obvious & simple, go ahead and do it. |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. The SNP is present in both files, but IGB only finds it in one of the files. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring |
| Attachment | GFF3_example_1_EDITED.gff3 [ 14247 ] |
| Attachment | AfterFix.jpg [ 14252 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Resolution | Done [ 10000 ] | |
| Status | Reviewing [ 10301 ] | Closed [ 6 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Workflow | Loraine Lab Workflow [ 16980 ] | Fall 2019 Workflow Update [ 19764 ] |
| Comment | [ We will review current architecture & discuss re-factoring, using this branch as an extremely useful proof-of-concept and guide. ] |
| Workflow | Fall 2019 Workflow Update [ 19764 ] | Revised Fall 2019 Workflow Update [ 21883 ] |
| Labels | Beginner | Advanced |