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  1. Bug Repository
  2. BUG-232

support SAM as well as BAM

          Details

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

            Description

            Support SAM as well as BAM. Load and visualize a sam file to ensure this works

            Open homo sapiens, go to chr Y. Download attached file to desktop, then drag into IGB. Reload (whole chromosome is fine since the sam file is tiny). Be sure that the sam file loads (insertions are seen as red lines within a read).

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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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                  ann.loraine Ann Loraine created issue -
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Done. Test it out.

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                  hiralv Hiral Vora (Inactive) added a comment - Done. Test it out.
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  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 -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Description Support SAM as well as BAM. Support SAM as well as BAM.

                  Load and visualize a sam file to ensure this works
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB6.6 [ 10021 ] Bug Repository [ 10030 ]
                  Key IGBA-33 BUG-232
                  Issue Type New Feature [ 2 ] Bug [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ]
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  passed mac in version 9804.

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                  alyssa Alyssa Gulledge (Inactive) added a comment - passed mac in version 9804.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Katharine Kubiak [ kkubiak ]
                  Attachment hg19Paired101bpChrYInsertions.sam.gz [ 10567 ]
                  Description Support SAM as well as BAM.

                  Load and visualize a sam file to ensure this works                   		Support SAM as well as BAM. Load and visualize a sam file to ensure this works

                  Open homo sapiens, go to chr Y. Download attached file to desktop, then drag into IGB. Reload (whole chromosome is fine since the sam file is tiny). Be sure that the sam file loads (insertions are seen as red lines within a read).
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Comment [ Do not have a SAM file to test ]
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9889 Windows

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                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9889 Windows
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] 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 ]
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Fuquan Wang [ fwang4 ]
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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  Passed on 7.0.0 (11884) Mac.

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                  fwang4 Fuquan Wang (Inactive) added a comment - Passed on 7.0.0 (11884) Mac.
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Fuquan Wang [ fwang4 ]
                  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 -
                  Status Reopened [ 4 ] Closed [ 6 ]
                  Resolution Fixed [ 1 ]

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      ann.loraine Ann Loraine
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                      Dates

                      • Created:
                        Updated:
                        Resolved: