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  1. IGB
  2. IGBF-1344

graph operations don't handle inverse 0 well

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          0.25
        • Epic Link:
        • 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

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2134 Fix inverse graph operation problem

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1340 Inverse,Log3,Natural Log operation of Track Graph did not show the same result as mentioned in the test wiki doc.

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1342 Diff operation on 2 tracks is giving " no point" in ycord value in selection info in Graph Track Operations

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ieclabau Ivory Blakley (Inactive) created issue -
                ieclabau Ivory Blakley (Inactive) made changes -
                Field Original Value New Value
                Link This issue relates to IGBF-1342 [ IGBF-1342 ]
                ieclabau Ivory Blakley (Inactive) made changes -
                Link This issue relates to IGBF-1340 [ IGBF-1340 ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18036 ] Fall 2019 Workflow Update [ 18883 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 18883 ] Revised Fall 2019 Workflow Update [ 21010 ]
                Status Open [ 1 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2134 [ IGBF-2134 ]
                nfreese Nowlan Freese made changes -
                Attachment graphWithNoZero.bedgraph [ 14929 ]
                Attachment graphWithZero.bedgraph [ 14930 ]
                nfreese Nowlan Freese made changes -
                Epic Link IGBF-1765 [ 17855 ]
                Hide
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                nfreese Nowlan Freese added a comment -

                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.

                Show
                nfreese Nowlan Freese added a comment - 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.
                nfreese Nowlan Freese made changes -
                Sprint Fall 4 Oct 26 - Nov 6 [ 107 ]
                nfreese Nowlan Freese made changes -
                Labels beginner
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                nfreese Nowlan Freese added a comment -

                [~aloraine] - 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.

                Show
                nfreese Nowlan Freese added a comment - [~aloraine] - 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.
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ]
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Assignee Sai Supreeth Segu [ ssegu ]
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Attachment graphWithNegative.bedgraph [ 14935 ]
                Hide
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                ssegu Sai Supreeth Segu (Inactive) added a comment -

                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

                Show
                ssegu Sai Supreeth Segu (Inactive) added a comment - 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
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Assignee Sai Supreeth Segu [ ssegu ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 Oct 26 - Nov 6 [ 107 ] Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20 [ 107, 108 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                noor91zahara Noor Zahara (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                noor91zahara Noor Zahara (Inactive) made changes -
                Assignee Noor Zahara [ noor91zahara ]
                noor91zahara Noor Zahara (Inactive) made changes -
                Assignee Noor Zahara [ noor91zahara ]
                noor91zahara Noor Zahara (Inactive) made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Story Points 0.25
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                Hide
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                nfreese Nowlan Freese added a comment -

                Sai Supreeth Segu - can you get rid of the commented out code from your commit?

                Show
                nfreese Nowlan Freese added a comment - Sai Supreeth Segu - can you get rid of the commented out code from your commit?
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Sai Supreeth Segu [ ssegu ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                Hide
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                ssegu Sai Supreeth Segu (Inactive) added a comment - - edited

                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

                Show
                ssegu Sai Supreeth Segu (Inactive) added a comment - - edited 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
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Sai Supreeth Segu [ ssegu ] Nowlan Freese [ nfreese ]
                Hide
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                nfreese Nowlan Freese added a comment -

                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.

                Show
                nfreese Nowlan Freese added a comment - 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.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Sai Supreeth Segu [ ssegu ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                Hide
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                ssegu Sai Supreeth Segu (Inactive) added a comment - - edited

                [~aloraine] - 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

                Show
                ssegu Sai Supreeth Segu (Inactive) added a comment - - edited [~aloraine] - 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
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Assignee Sai Supreeth Segu [ ssegu ]
                Hide
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                ssegu Sai Supreeth Segu (Inactive) added a comment -

                Dr. [~aloraine] 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

                Show
                ssegu Sai Supreeth Segu (Inactive) added a comment - Dr. [~aloraine] 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
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                ann.loraine Ann Loraine added a comment -

                Nowlan Freese - please confirm that the requested functionality is implemented in released IGB version 9.1.6.

                Show
                ann.loraine Ann Loraine added a comment - Nowlan Freese - please confirm that the requested functionality is implemented in released IGB version 9.1.6.
                ann.loraine Ann Loraine made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Hide
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                nfreese Nowlan Freese added a comment -

                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.

                Show
                nfreese Nowlan Freese added a comment - 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.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Sai Supreeth Segu [ ssegu ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    ssegu Sai Supreeth Segu (Inactive)
                    Reporter:
                    ieclabau Ivory Blakley (Inactive)
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    4 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: