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  1. Bug Repository
  2. BUG-598

View Read Sequence in sequence viewer of INSERTED short reads is completely wrong

          Details

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

            Description

            "View read Sequence" on an inserted short read puts the Reverse Complement of the genomic sequence into the viewer. It does NOT give the inserted read sequence.

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                Issue Links

                relates to

                Task - A task that needs to be done. BUG-608 Sequence viewer bugs

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

                  Activity

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                  alyssa Alyssa Gulledge (Inactive) created issue -
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Hiral Vora [ hiralv ] Fuquan Wang [ fwang4 ]
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Fuquan Wang [ fwang4 ] Hiral Vora [ hiralv ]
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Fuquan Wang [ fwang4 ]
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r13408.

                  Note:
                  (Fixed cigar parsing in r13402, Added insert residue in sequence viewer in r13404 and kept child order based on minimum value in r13408)

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                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r13408. Note: (Fixed cigar parsing in r13402, Added insert residue in sequence viewer in r13404 and kept child order based on minimum value in r13408)
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Fuquan Wang [ fwang4 ] Alyssa Gulledge [ alyssa ]
                  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-483 BUG-598
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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  Also disabled the view seq option for insertion in 13431.

                  Show
                  fwang4 Fuquan Wang (Inactive) added a comment - Also disabled the view seq option for insertion in 13431.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-26 [ BUG-26 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-608 [ BUG-608 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-26 [ BUG-26 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Assignee Richard Linchangco [ richard ]
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                  richard Richard Linchangco (Inactive) added a comment -

                  Please attach files

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Please attach files
                  richard Richard Linchangco (Inactive) made changes -
                  Assignee Richard Linchangco [ richard ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Attachment hg19Paired101bpChrYDeletions.bai [ 11660 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Attachment hg19Paired101bpChrYDeletions.bam [ 11661 ]
                  Attachment hg19Paired101bpChrYInsertions.bai.zip [ 11662 ]
                  Attachment hg19Paired101bpChrYInsertions.bam.zip [ 11663 ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  To use these files: download all, open the zips. The bai file (index file) must be kept in the same folder/location as the bam files. However, just drag and drop the bam file into IBG. Notably for these two files, open H. Sapiens, most recent genome, go to chromosome Y and then load these.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - To use these files: download all, open the zips. The bai file (index file) must be kept in the same folder/location as the bam files. However, just drag and drop the bam file into IBG. Notably for these two files, open H. Sapiens, most recent genome, go to chromosome Y and then load these.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Richard Linchangco [ richard ]
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13551, Mac, Java 1.06.0_37
                  Posted Insertion file becomes corrupted after unzipping. Used file provided by Alyssa

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13551, Mac, Java 1.06.0_37 Posted Insertion file becomes corrupted after unzipping. Used file provided by Alyssa
                  richard Richard Linchangco (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Richard Linchangco [ richard ] Alyssa Gulledge [ alyssa ]
                  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 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Closed [ 6 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]

                    People

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

                      • Created:
                        Updated:
                        Resolved: