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  1. IGB
  2. IGBF-1468

Implement better handling of CIGAR string in BAM/SAM

        Details

        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov

          Description

          Working with PacBio long reads from a URL, hit a SocketTimeoutException. The reads do not display correctly - appearing as unfilled squares. The read scores also seem to be incorrect, though that may be a separate issue.

          Example bam can be found here

            Attachments

            1. 1 (1).txt
              68 kB
            2. exception.txt
              5 kB
            3. igb.png
              igb.png
              123 kB
            4. pacBio.bam
              1.11 MB
            5. pacBio.bam.bai
              1 kB
            6. pacBio-OneRead_42EQUALS.bam
              6 kB
            7. pacBio-OneRead_42EQUALS.bam.bai
              0.8 kB
            8. pacBio-OneRead_42X.bam
              6 kB
            9. pacBio-OneRead_42X.bam.bai
              0.8 kB
            10. pacBio-OneRead_5224S42EQUALS.bam
              9 kB
            11. pacBio-OneRead_5224S42EQUALS.bam.bai
              0.8 kB
            12. pacBio-OneRead_5224S42M.bam
              9 kB
            13. pacBio-OneRead_5224S42M.bam.bai
              0.8 kB
            14. pacBio-OneRead.bam
              14 kB
            15. pacBio-OneRead.bam.bai
              0.8 kB
            16. readExample.txt
              19 kB
            17. Screen Shot 2018-11-26 at 5.13.51 PM.png
              Screen Shot 2018-11-26 at 5.13.51 PM.png
              227 kB

              Activity

                People

                • Assignee:
                  noor91zahara Noor Zahara (Inactive)
                  Reporter:
                  nfreese Nowlan Freese
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                  Dates

                  • Created:
                    Updated:
                    Resolved: