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  1. IGB
  2. IGBF-2978

Improve bigBed parsing

        Details

        • Story Points:
          4
        • Epic Link:
        • Sprint:
          Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14

          Description

          Situation: bigBed is an indexed binary format of bed files. However, in IGB, bigBed files are not appearing correctly. The bigBed gene annotations (see attached file) are not showing the introns/exons, but instead are drawing a single glyph for the entire gene.

          Task: Fix IGB so that the bigBed files appear correctly.

          See the UCSC guide on bigBed for more information on the bigBed file format.

            Attachments

            1. Araport11.bb
              3.14 MB
            2. bbVSbed.png
              bbVSbed.png
              149 kB
            3. bed.png
              bed.png
              195 kB
            4. bed and bb.png
              bed and bb.png
              80 kB
            5. bedDetail.as
              0.9 kB
            6. chrom.sizes
              0.1 kB

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2979 Investigate: bigBed chromosome synonyms logic

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-2954 Investigate: why is loading bb (bigbed) and bigwig (bw) files so slow?

              • Major - Major loss of function.
              • Closed

                Activity

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                11 older comments
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                omarne Omkar Marne (Inactive) added a comment - - edited

                I installed 2978 branch installer and uploaded both the files mentioned above. The results are as expected.

                There are errors or warnings in the log.

                Ticket is ready for the pull request.

                Show
                omarne Omkar Marne (Inactive) added a comment - - edited I installed 2978 branch installer and uploaded both the files mentioned above. The results are as expected. There are errors or warnings in the log. Ticket is ready for the pull request.
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                nfreese Nowlan Freese added a comment -

                Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/892

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                nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/892
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                ann.loraine Ann Loraine added a comment - - edited

                Merged. Building master branch installers. Master branch installers built and also deployed on bioviz main in "early access igb" section.

                Ready for testing.

                Show
                ann.loraine Ann Loraine added a comment - - edited Merged. Building master branch installers. Master branch installers built and also deployed on bioviz main in "early access igb" section. Ready for testing.
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                omarne Omkar Marne (Inactive) added a comment - - edited

                I installed 2978 branch installer and uploaded both the files mentioned above. The results are as expected. The exons and introns are same.

                There are errors or warnings in the log.

                Closing the ticket.

                Show
                omarne Omkar Marne (Inactive) added a comment - - edited I installed 2978 branch installer and uploaded both the files mentioned above. The results are as expected. The exons and introns are same. There are errors or warnings in the log. Closing the ticket.
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                nfreese Nowlan Freese added a comment -

                If you are looking for example .as (autosql) files check out the following links:
                https://github.com/ucscGenomeBrowser/kent/tree/e01be94b2df0b6b467170df7e304ed87493317bd/src/hg/lib
                https://genome-source.gi.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/

                Show
                nfreese Nowlan Freese added a comment - If you are looking for example .as (autosql) files check out the following links: https://github.com/ucscGenomeBrowser/kent/tree/e01be94b2df0b6b467170df7e304ed87493317bd/src/hg/lib https://genome-source.gi.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: