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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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                  hiralv Hiral Vora (Inactive) created issue -
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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.
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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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.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB6.6 [ 10021 ] Bug Repository [ 10030 ]
                  Key IGBA-234 BUG-177
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Katharine Kubiak [ kkubiak ]
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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
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Anuj Puram [ anuj ]
                  Hide
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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
                  anuj Anuj Puram (Inactive) made changes -
                  Assignee Anuj Puram [ anuj ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Vineeth Mylapur [ smylapur ]
                  Hide
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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.
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Vineeth Mylapur [ smylapur ]
                  Resolution Fixed [ 1 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-622 [ BUG-622 ]
                  Hide
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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)
                  Hide
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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)
                  richard Richard Linchangco (Inactive) made changes -
                  Attachment SGRworks.png [ 11758 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Hide
                  Permalink
                  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
                  richard Richard Linchangco (Inactive) made changes -
                  Attachment largeSGRfile.png [ 11763 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  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. 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.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Closed [ 6 ]
                  Resolution Fixed [ 1 ]

                    People

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

                      • Created:
                        Updated:
                        Resolved: