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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.

              Attachments

              1. hg19Paired101bpChrYDeletions.bai
                30 kB
                Alyssa Gulledge
              2. hg19Paired101bpChrYDeletions.bam
                19 kB
                Alyssa Gulledge

                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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                  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)
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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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                  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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                  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 -

                  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

                    People

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

                      • Created:
                        Updated:
                        Resolved: