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  1. Bug Repository
  2. BUG-627

IGB shows gff3 perfectly, but the SAVE function creates bed/bedDetail files that are wrong

          Details

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

            Description

            Somehow the bed files lose the intron/exon information - see attached picture. This is a stopper for Anuj's file converter.

              Attachments

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-624 File Menu items

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

                  Activity

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                  alyssa Alyssa Gulledge (Inactive) created issue -
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Can you send me this file?

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                  hiralv Hiral Vora (Inactive) added a comment - Can you send me this file?
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB 6.7 [ 10040 ] IGB 7.0 [ 10140 ]
                  Key IGBB-390 IGBC-777
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Attachment test1.bed [ 11658 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Attachment ChLGX_official_gene.gff3 [ 11659 ]
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r13530.

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                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r13530.
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Looks good. Anuj - do you need to change anything for your converter program?

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Looks good. Anuj - do you need to change anything for your converter program?
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Anuj Puram [ anuj ]
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                  anuj Anuj Puram (Inactive) added a comment -

                  Made Changes and uploaded the new JNLP at
                  http://test.bioviz.org/BedConversion/

                  Show
                  anuj Anuj Puram (Inactive) added a comment - Made Changes and uploaded the new JNLP at http://test.bioviz.org/BedConversion/
                  anuj Anuj Puram (Inactive) made changes -
                  Assignee Anuj Puram [ anuj ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Still giving me the broken bed files

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                  alyssa Alyssa Gulledge (Inactive) added a comment - Still giving me the broken bed files
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Anuj Puram [ anuj ]
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                  anuj Anuj Puram (Inactive) added a comment -

                  I uploaded the updated jnlp

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                  anuj Anuj Puram (Inactive) added a comment - I uploaded the updated jnlp
                  anuj Anuj Puram (Inactive) made changes -
                  Assignee Anuj Puram [ anuj ] Alyssa Gulledge [ alyssa ]
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                  anuj Anuj Puram (Inactive) added a comment -

                  I uploaded the updated Jnlp at http://test.bioviz.org/BedConversion/
                  I even fixed the issue of the name extension

                  Show
                  anuj Anuj Puram (Inactive) added a comment - I uploaded the updated Jnlp at http://test.bioviz.org/BedConversion/ I even fixed the issue of the name extension
                  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 IGB 7.0 [ 10140 ] Bug Repository [ 10030 ]
                  Key IGBC-777 BUG-627
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-624 [ BUG-624 ]

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: