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  1. IGB
  2. IGBF-1098

Update BAM, tabix reader libraries

        Details

        • Story Points:
          1
        • Sprint:
          B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3

          Description

          We need to upgrade our sam/bam parsing library to be in line with the updated sam/bam specification. Currently some header flags which are part of the specification (i.e. SO) will cause exceptions to be thrown by the samtools libary and prevent the ability of users to load their data.

          We should update our libary and parsers to resolve the issue.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-1321 Test for errors due to htsjdk library update

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-1417 Create new artifact with bigbed and bigwig parsing code from IGV codebase

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1418 Import htsjdk as OSGi bundle

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1699 Remove unneeded dependencies from modules

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-1321 Test for errors due to htsjdk library update

              • Major - Major loss of function.
              • Closed

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                  People

                  • Assignee:
                    kkorey Kiran Korey (Inactive)
                    Reporter:
                    dcnorris David Norris (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: