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  1. IGB
  2. IGBF-706

BAM read labels may be shown even when Label Field is set to "none"

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Ann noticed that BAM read labels may be shown even when Label Field is set to "none".

          This may be related to local BAM files only.

          We should test further to determine ways to reliably reproduce this problem.

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              mason Mason Meyer (Inactive) created issue -
              mason Mason Meyer (Inactive) made changes -
              Field Original Value New Value
              Epic Link IGBF-497 [ 15559 ]
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              ann.loraine Ann Loraine added a comment -

              To reproduce:

              1. Download attached BAM and BAI files, save into the same location (e.g., Desktop)
              2. Go to latest tomato genome
              3. Open BAM file
              4. Go to SL2.50ch00:11,950,779-11,952,970
              5. Load data

              Note: the file is very small so you can load the data even when the entire chromosome SL2.50ch00 is being shown.

              6. Observe that read names are displayed (see attached)

              Show
              ann.loraine Ann Loraine added a comment - To reproduce: 1. Download attached BAM and BAI files, save into the same location (e.g., Desktop) 2. Go to latest tomato genome 3. Open BAM file 4. Go to SL2.50ch00:11,950,779-11,952,970 5. Load data Note: the file is very small so you can load the data even when the entire chromosome SL2.50ch00 is being shown. 6. Observe that read names are displayed (see attached)
              ann.loraine Ann Loraine made changes -
              Attachment LittleTomatoBam.bam [ 13082 ]
              Attachment LittleTomatoBam.bam.bai [ 13083 ]
              ann.loraine Ann Loraine made changes -
              Attachment igb.png [ 13084 ]
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              ann.loraine Ann Loraine added a comment -

              Also, select the track showing the BAM file and select the Annotation tab.

              Observe that Label Field options are limited - they list "name" "type" and "none"

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              ann.loraine Ann Loraine added a comment - Also, select the track showing the BAM file and select the Annotation tab. Observe that Label Field options are limited - they list "name" "type" and "none"
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              dcnorris David Norris (Inactive) added a comment -

              Could not reproduce

              Show
              dcnorris David Norris (Inactive) added a comment - Could not reproduce
              mason Mason Meyer (Inactive) made changes -
              Rank Ranked higher
              mason Mason Meyer (Inactive) made changes -
              Sprint Backlog Grooming Meeting [ 29 ] Sprint 21 [ 26 ]
              mason Mason Meyer (Inactive) made changes -
              Rank Ranked lower
              mason Mason Meyer (Inactive) made changes -
              Status Open [ 1 ] Testing In Progress [ 10003 ]
              mason Mason Meyer (Inactive) made changes -
              Assignee Mason Meyer [ mason ]
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              mason Mason Meyer (Inactive) added a comment -

              This issue has been resolved with the fix for IGBF-709. Since this issue is resolved it will now be closed.

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              mason Mason Meyer (Inactive) added a comment - This issue has been resolved with the fix for IGBF-709 . Since this issue is resolved it will now be closed.
              mason Mason Meyer (Inactive) made changes -
              Resolution Done [ 10000 ]
              Status Testing In Progress [ 10003 ] Closed [ 6 ]
              ann.loraine Ann Loraine made changes -
              Workflow Loraine Lab Workflow [ 16002 ] Fall 2019 Workflow Update [ 19520 ]
              ann.loraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 19520 ] Revised Fall 2019 Workflow Update [ 21637 ]

                People

                • Assignee:
                  mason Mason Meyer (Inactive)
                  Reporter:
                  mason Mason Meyer (Inactive)
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                  Dates

                  • Created:
                    Updated:
                    Resolved: