Details
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Type:
Bug
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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: None
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Labels:
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Story Points:0.25
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Epic Link:
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Sprint:Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5
Description
Graph tracks can have regions with value=0.
One of the graph track operations is the inverse function, and several other functions include an inverse.
But the inverse of 0 is infinity.
IGB needs to handle this.
Currently, if you take the inverse of a graph track where the value is 0, the y-max for the resulting track is set to 340282346638528860000000000000000000000, and the values on the Y-axis end in "Y", and all the values that have legit values are squished down to be invisible, so the entire track appears blank.
The inverse function just needs to have a catch to handle this. If input is 0, output is NA.
Attachments
Issue Links
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Activity
| Workflow | Loraine Lab Workflow [ 18036 ] | Fall 2019 Workflow Update [ 18883 ] |
| Workflow | Fall 2019 Workflow Update [ 18883 ] | Revised Fall 2019 Workflow Update [ 21010 ] |
| Status | Open [ 1 ] | To-Do [ 10305 ] |
| Attachment | graphWithNoZero.bedgraph [ 14929 ] | |
| Attachment | graphWithZero.bedgraph [ 14930 ] |
| Epic Link | IGBF-1765 [ 17855 ] |
| Sprint | Fall 4 Oct 26 - Nov 6 [ 107 ] |
| Labels | beginner |
Ann Loraine - I have not looked at the underlying code, but the idea at least is simple and is easy to test. I added instructions for replicating the issue in IGB and have added example files to test. I've added the beginner tag for now.
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | graphWithNegative.bedgraph [ 14935 ] |
I have changed the value to 0.
Link for the code change: https://bitbucket.org/supreeth27/integrated-genome-browser/branch/IGBF-1344#diff
Please review it
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Sprint | Fall 4 Oct 26 - Nov 6 [ 107 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20 [ 107, 108 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Story Points | 0.25 |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Sai Supreeth Segu - can you get rid of the commented out code from your commit?
| Assignee | Nowlan Freese [ nfreese ] | Sai Supreeth Segu [ ssegu ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
Nowlan Freese - I have removed the commented code. Please have a look at it.
Link for code change: https://bitbucket.org/supreeth27/integrated-genome-browser/branch/IGBF-1344#diff
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] | Nowlan Freese [ nfreese ] |
Tested on mac using 1344 dmg installer from Supreeth's branch.
Tested using attached test files. Working correctly.
Sai Supreeth Segu ready for pull request.
| Assignee | Nowlan Freese [ nfreese ] | Sai Supreeth Segu [ ssegu ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Ann Loraine - Please review my pull request
Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/849/igbf-1344-fixing-inverse-0-value
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
Dr. Ann Loraine and Dr. Nowlan Freese, I have updated the pull request with a commit. Please review the pull request.
Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/849/igbf-1344-fixing-inverse-0-value
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20 [ 107, 108 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 23 - Dec 4 [ 107, 108, 109 ] |
| Rank | Ranked higher |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11 [ 107, 108, 109 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 107, 108, 109, 110 ] |
| Rank | Ranked higher |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 107, 108, 109, 110 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 107, 108, 109, 110, 111 ] |
| Rank | Ranked higher |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 107, 108, 109, 110, 111 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 107, 108, 109, 110, 111, 112 ] |
| Rank | Ranked higher |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 107, 108, 109, 110, 111, 112 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 107, 108, 109, 110, 111, 112, 113 ] |
| Rank | Ranked higher |
Nowlan Freese - please confirm that the requested functionality is implemented in released IGB version 9.1.6.
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Tested on release 9.1.6 on Mac using the attached bedgraph files.
Applying inverse to a value of 0 in the graph operations now results in a value of infinity.
Closing issue.
| Assignee | Nowlan Freese [ nfreese ] | Sai Supreeth Segu [ ssegu ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
To replicate in IGB:
1) Open human genome (H_sapiens_Dec_2013)
2) Navigate to: chr1:0-550
3) Load the two attached files (graphWithNoZero.bedgraph and graphWithZero.bedgraph) into IGB and load their data.
4) Click the graphWithZero.bedgraph track label to select it.
5) Under the Graph tab within the Operations section, change the Single-Graph dropdown to Inverse and click Go.
Note that this will max out the value of the zero values to 340282346638528860000000000000000000000.
Repeat the same steps for the graphWithNoZero.bedgraph file to observe how the graph should appear.