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  1. IGB
  2. IGBF-4106

Integrate htsjdk library for parsing VCF in IGB

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: 10.2.0
        • Labels:
          None

          Description

          Situation: VCF file is being read line by line manually

          Task: Investigate how we could integrate htsjdk library to make use of in-built classes instead of manual processing of vcf file

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-4082 Investigate: How is IGB parsing and displaying VCF files?

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-4083 Investigate: How is IGV parsing and displaying VCF files?

              • Major - Major loss of function.
              • Closed
              is cloned by

              Task - A task that needs to be done. IGBF-4153 Eliminate lineProcessor implementation in VCF loader in IGB

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-4219 Fix loading remote VCF files

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                sjagarap saideepthi jagarapu (Inactive) created issue -
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Field Original Value New Value
                Epic Link IGBF-3836 [ 23135 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Summary Investigate integrating htsjdk library for parsing VCF in IGB Investigate: Integrating htsjdk library for parsing VCF in IGB
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Sprint Spring 3 [ 212 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Link This issue blocks IGBF-4082 [ IGBF-4082 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Link This issue blocks IGBF-4083 [ IGBF-4083 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3 [ 212 ] Spring 3, Spring 4 [ 212, 213 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Link This issue is cloned by IGBF-4153 [ IGBF-4153 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3, Spring 4 [ 212, 213 ] Spring 3, Spring 4, Spring 5 [ 212, 213, 214 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3, Spring 4, Spring 5 [ 212, 213, 214 ] Spring 3, Spring 4, Spring 5, Spring 6 [ 212, 213, 214, 215 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Summary Investigate: Integrating htsjdk library for parsing VCF in IGB Integrate htsjdk library for parsing VCF in IGB
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Link This issue relates to IGBF-4219 [ IGBF-4219 ]
                pkulzer Paige Kulzer (Inactive) made changes -
                Fix Version/s 10.2.0 [ 11100 ]

                  People

                  • Assignee:
                    sjagarap saideepthi jagarapu (Inactive)
                    Reporter:
                    sjagarap saideepthi jagarapu (Inactive)
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: