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  1. Bug Repository
  2. BUG-177

SGR file format broken

          Details

          • Type: Bug
          • Status: Closed (View Workflow)
          • Priority: Major
          • Resolution: Fixed
          • Labels:
            None

            Description

            Large sgr files (40000 points on one chromosome) are not displayed properly in IGB versions 6.3 or later, but they are in versions 6.22 or earlier. The display is incorrect in styles stairStep, dot and bar, but correct in the other styles. The problem is that the data for the right end of the chromosome is not displayed, or maybe the numbering is off and it is compressed. I think it does work properly for smaller numbers of data points. The problem is only seen when you are displaying a big chunk or entire chromosome, and it seems to be correct when you zoom in enough.

            To test, load H sapiens 2006, then load SGR. change through each graph type and ensure full coverage.

              Attachments

              1. bdebffgb.png
                77 kB
              2. hgfjbgca.png
                73 kB
              3. largeSGRfile.png
                189 kB
              4. PGG63_LRR_chr1.sgr.gz
                318 kB
              5. SGRworks.png
                121 kB

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-622 File format issues

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13655, Mac, Java 1.06.0_37

                  See attached photo (sgr load working): largeSGRfile.png

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13655, Mac, Java 1.06.0_37 See attached photo (sgr load working): largeSGRfile.png
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                  richard Richard Linchangco (Inactive) added a comment -

                  Functioning SGR image. Mac, IGB 7.0(13526)

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Functioning SGR image. Mac, IGB 7.0(13526)
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13526, Mac, Java 1.06.0_37

                  Image attached for comparison on IGB 7.0(13526)

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13526, Mac, Java 1.06.0_37 Image attached for comparison on IGB 7.0(13526)
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                  smylapur Vineeth Mylapur (Inactive) added a comment -

                  Passed 7.0 (11934) on windows.

                  Show
                  smylapur Vineeth Mylapur (Inactive) added a comment - Passed 7.0 (11934) on windows.
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                  anuj Anuj Puram (Inactive) added a comment -

                  Passed v9906 on Mac

                  Show
                  anuj Anuj Puram (Inactive) added a comment - Passed v9906 on Mac
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9818 Windows

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9818 Windows
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Check it on branch.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Check it on branch.
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r9288.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r9288.

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      hiralv Hiral Vora (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: