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  1. IGB
  2. IGBF-3032

Change default name for bookmarks

    Details

    • Story Points:
      0.25
    • Sprint:
      Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28

      Description

      Currently, bookmark "default name" looks like:

      H_sapiens_Dec_2013, chr1 : 0 - 248,956,422

      The "default name" is getting constructed from the genome name (e.g., H_sapiens_Dec_2013), the currently viewed chromosome (e.g., chr1), and the currently visible region (e.g., 0 - 248,956,422).

      The format of the default name is OK, but it would be more useful if it used a format accepted by the "samtools view" command. (Samtools is a very popular program in bioinformatics.)

      Samtools view accepts a region string that looks like:

      chr1:0-248,956,422

      Note it is very similar to our current "default" name, but ours contains space characters.

      Let's modify our "default" name to look like what samtools view accepts, by removing the space characters in the region string part.

      For example:

      H_sapiens_Dec_2013, chr1 : 0 - 248,956,422

      will be instead:

      H_sapiens_Dec_2013, chr1:0-248,956,422

      Please change the format so that the "default name" is

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            omarne Omkar Marne (Inactive) added a comment - - edited Dr. [~aloraine] Please find my new pull request : https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/895/igbf-3032-new-name-format-for-bookmark
            Hide
            ann.loraine Ann Loraine added a comment -

            PR is merged. Building master branch installers.

            Show
            ann.loraine Ann Loraine added a comment - PR is merged. Building master branch installers.
            Hide
            ann.loraine Ann Loraine added a comment -

            Master branch installers are deployed to the IGB early access section of bioviz main Web site. Ready for testing.

            Show
            ann.loraine Ann Loraine added a comment - Master branch installers are deployed to the IGB early access section of bioviz main Web site. Ready for testing.
            Hide
            omarne Omkar Marne (Inactive) added a comment - - edited

            Testing protocol:

            • Please pull the latest changes made in the IGB code.
            • Open IGB local environment and select any genome
            • Open the bookmark menu.
            • The format of the default bookmark name should be like H_sapiens_Dec_2013, chr1:0-248,956,422 instead of H_sapiens_Dec_2013, chr1 : 0 - 248,956,422.
            • The spaces between the numbers and before and after colon have been removed.
            Show
            omarne Omkar Marne (Inactive) added a comment - - edited Testing protocol: Please pull the latest changes made in the IGB code. Open IGB local environment and select any genome Open the bookmark menu. The format of the default bookmark name should be like H_sapiens_Dec_2013, chr1:0-248,956,422 instead of H_sapiens_Dec_2013, chr1 : 0 - 248,956,422. The spaces between the numbers and before and after colon have been removed.
            Hide
            nfreese Nowlan Freese added a comment -

            Tested on Mac, working correctly, no errors in log.

            Closing ticket.

            Show
            nfreese Nowlan Freese added a comment - Tested on Mac, working correctly, no errors in log. Closing ticket.

              People

              • Assignee:
                omarne Omkar Marne (Inactive)
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
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                3 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: