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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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                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

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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

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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
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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.
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                  richard Richard Linchangco (Inactive) added a comment -

                  Please attach files

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                  richard Richard Linchangco (Inactive) added a comment - Please attach files
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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  Also disabled the view seq option for insertion in 13431.

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                  fwang4 Fuquan Wang (Inactive) added a comment - Also disabled the view seq option for insertion in 13431.
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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)

                    People

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

                      • Created:
                        Updated:
                        Resolved: