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  1. Bug Repository
  2. BUG-106

Identical file name generates a merged track.

          Details

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

            Description

            To reproduce: Load A thal 2009. Load CoolL1T1.sm.bam from http://transvar.org/illumina/tophat_3_processed/. Load the same file from http://transvar.org/illumina/tophat-1.1.4-heat-drought-processed/

            IGB lists them separately in the 'Load Mode' list.

            Zoom in and refresh - they load into one track, even though the files contain different data and they come from different web addresses.

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

                  Also, if you then delete one file, the track goes away; then when you hit refresh to reload the remaiing file, nothing happens.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Also, if you then delete one file, the track goes away; then when you hit refresh to reload the remaiing file, nothing happens.
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed.
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Still not working for me on v. 8129

                  Same test, same problem

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Still not working for me on v. 8129 Same test, same problem
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in 8131.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in 8131.
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  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-49 BUG-106
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                  ann.loraine Ann Loraine added a comment - - edited

                  Test what happens with files of different types, e.g.,

                  CoolHT1.sm.bam
                  CoolHT1.sm.wig

                  from transvar.org/illumina/tophat_3

                  Show
                  ann.loraine Ann Loraine added a comment - - edited Test what happens with files of different types, e.g., CoolHT1.sm.bam CoolHT1.sm.wig from transvar.org/illumina/tophat_3
                  Hide
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                  ann.loraine Ann Loraine added a comment -

                  Test on trunk and 6.5.1. branch.

                  Show
                  ann.loraine Ann Loraine added a comment - Test on trunk and 6.5.1. branch.
                  ann.loraine Ann Loraine made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  imnick Nick Ren (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ]
                  imnick Nick Ren (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  imnick Nick Ren (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  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 v9844 Windows

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9844 Windows
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Anuj Puram [ anuj ]
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                  anuj Anuj Puram (Inactive) added a comment -

                  Passed 6.7.0 (9891) on Mac

                  Show
                  anuj Anuj Puram (Inactive) added a comment - Passed 6.7.0 (9891) 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 ]
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                  smylapur Vineeth Mylapur (Inactive) added a comment -

                  Second link is not working.

                  Show
                  smylapur Vineeth Mylapur (Inactive) added a comment - Second link is not working.
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Assignee Vineeth Mylapur [ smylapur ] Alyssa Gulledge [ alyssa ]
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                  kkubiak Katharine Kubiak (Inactive) added a comment - - edited

                  You can use BA2.sm.bam from http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/ngs/cyto_processed/ and from http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/ngs/tophat_4_processed/?C=S;O=A

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - - edited You can use BA2.sm.bam from http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/ngs/cyto_processed/ and from http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/ngs/tophat_4_processed/?C=S;O=A
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Vineeth Mylapur [ smylapur ]
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                  smylapur Vineeth Mylapur (Inactive) added a comment -

                  Passed 7.0 (11923) on windows

                  Show
                  smylapur Vineeth Mylapur (Inactive) added a comment - Passed 7.0 (11923) 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 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-623 [ BUG-623 ]
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13621, Mac, Java 1.06.0_37
                  Tested same file types, different file types.

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13621, Mac, Java 1.06.0_37 Tested same file types, different file types.
                  richard Richard Linchangco (Inactive) made changes -
                  Link This issue relates to BUG-623 [ BUG-623 ]
                  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
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13655, Mac, Java 1.06.0_37

                  Tested exact same file names and type:

                  Tested same file name, different file type:

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13655, Mac, Java 1.06.0_37 Tested exact same file names and type: http://bioviz.org/filerepo/Quickload/A_thaliana_Jun_2009/cold_stress/cold_control.sm.bedgraph.gz http://igbquickload.org/quickload/A_thaliana_Jun_2009/cold_stress/cold_control.sm.bedgraph.gz Tested same file name, different file type: http://igbquickload.org/quickload/A_thaliana_Jun_2009/cold_stress/cold_treatment.sm.bam http://igbquickload.org/quickload/A_thaliana_Jun_2009/cold_stress/cold_treatment.sm.bedgraph.gz
                  richard Richard Linchangco (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]

                    People

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

                      • Created:
                        Updated:
                        Resolved: