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  1. IGB
  2. IGBF-1090

Implement saving of all chromosomes when exporting as bedgraph

        Details

        • Story Points:
          3
        • Sprint:
          Fall 2017

          Description

          A user requested that we add the ability to export data of all chromosomes in IGB when exporting a graph track (as a bedgraph file).

          We currently export data of all loaded chromosomes for annotations, but not graphs.

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              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1147 better bedgraph formatting

              • Major - Major loss of function.
              • In Progress

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1128 Save As... feature appends extra text that can cause the file name to be invalid

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1149 default file extension for graph tracks

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-144 Save all data and not just current chromosome for graphs

              • Major - Major loss of function.
              • Closed

                Activity

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                18 older comments
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                mason Mason Meyer (Inactive) added a comment - - edited

                #2 1st-Level Review:

                • Only the selected track saves for any chromosome that has been loaded.
                • Annotation tracks are being saved as expected with no header
                • Graph tracks have the same track name and color scheme as the original file

                Since this issue has been reviewed twice and passed the reviews, I am moving the issue to the Needs Pull Request Column and assigning the issue to Ivory.

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                mason Mason Meyer (Inactive) added a comment - - edited #2 1st-Level Review: Only the selected track saves for any chromosome that has been loaded. Annotation tracks are being saved as expected with no header Graph tracks have the same track name and color scheme as the original file Since this issue has been reviewed twice and passed the reviews, I am moving the issue to the Needs Pull Request Column and assigning the issue to Ivory.
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                mason Mason Meyer (Inactive) added a comment -

                While testing this story on the development branch I noticed that it was not functioning as expected because data was not being saved for ALL chromosomes in which data had been loaded. Is it possible that the code that made it to eos.transvar.org comes from Ivory's story IGBF-1090 instead of her working branch called IGBF-1090-b?

                To reproduce:

                1) Download and run IGB from http://eos.transvar.org/igb/
                2) Open A. thaliana genome and load some bedgraph data on Chr1 and Chr3
                3) Now Save the bedgraph track as a new file (do this from Chr3)
                4) Open th saved track in IGB and load data for Chr 1 and Chr 3.

                *Observe: There is no data on Chr 1 for the new track, but there should be.

                I am re-assinging this to Ivory and moving it back to the Reviewing Pull-Request column.

                Show
                mason Mason Meyer (Inactive) added a comment - While testing this story on the development branch I noticed that it was not functioning as expected because data was not being saved for ALL chromosomes in which data had been loaded. Is it possible that the code that made it to eos.transvar.org comes from Ivory's story IGBF-1090 instead of her working branch called IGBF-1090 -b? To reproduce: 1) Download and run IGB from http://eos.transvar.org/igb/ 2) Open A. thaliana genome and load some bedgraph data on Chr1 and Chr3 3) Now Save the bedgraph track as a new file (do this from Chr3) 4) Open th saved track in IGB and load data for Chr 1 and Chr 3. *Observe: There is no data on Chr 1 for the new track, but there should be. I am re-assinging this to Ivory and moving it back to the Reviewing Pull-Request column.
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                ieclabau Ivory Blakley (Inactive) added a comment -

                I just updated my master branch and tested. Like Mason said, data from a graph track is saved for ONLY the current chromosome, not for all loaded chromosomes.

                The most recent changes on branch IGBF-1090-b are not reflected in the current master branch.
                I searched in the commits for main master and I do not see any commit where branch IGBF-1090 or IGBF-1090-b was ever merged in.

                If you can give me the commit id or pull request number so I can see exactly what was merged in I can look into this further.
                My current best guess is that this branch never was merged into master.

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                ieclabau Ivory Blakley (Inactive) added a comment - I just updated my master branch and tested. Like Mason said, data from a graph track is saved for ONLY the current chromosome, not for all loaded chromosomes. The most recent changes on branch IGBF-1090 -b are not reflected in the current master branch. I searched in the commits for main master and I do not see any commit where branch IGBF-1090 or IGBF-1090 -b was ever merged in. If you can give me the commit id or pull request number so I can see exactly what was merged in I can look into this further. My current best guess is that this branch never was merged into master.
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                ieclabau Ivory Blakley (Inactive) added a comment -

                I rebased branch IGBF-1090-b from master, tested (still good) and submitted a pull request.

                Show
                ieclabau Ivory Blakley (Inactive) added a comment - I rebased branch IGBF-1090 -b from master, tested (still good) and submitted a pull request.
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                mason Mason Meyer (Inactive) added a comment -

                After testing, it seems the issue is resolved.

                *Only the selected track saves for any chromosome that has been loaded.
                *Annotation tracks are being saved as expected with no header
                *Graph tracks have the same track name and color scheme as the original file
                *I could not find any other side effects or issues related to this change.

                Since this issue is resolved, it will now be closed.

                Show
                mason Mason Meyer (Inactive) added a comment - After testing, it seems the issue is resolved. *Only the selected track saves for any chromosome that has been loaded. *Annotation tracks are being saved as expected with no header *Graph tracks have the same track name and color scheme as the original file *I could not find any other side effects or issues related to this change. Since this issue is resolved, it will now be closed.

                  People

                  • Assignee:
                    mason Mason Meyer (Inactive)
                    Reporter:
                    mason Mason Meyer (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: