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  1. IGB
  2. IGBF-4153

Eliminate lineProcessor implementation in VCF loader in IGB

        Details

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

          Description

          Situation: loaders depends on LineProcessor for parsing and loading genomic regions

          Task: Investigate how we could eliminate the LineProcessor dependency completely, streamlining the parsing process and displaying region.

            Attachments

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              clones

              Task - A task that needs to be done. IGBF-4106 Integrate htsjdk library for parsing VCF in IGB

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

              Task - A task that needs to be done. IGBF-4166 Collect VCF files and test new vcf parsing

              • Major - Major loss of function.
              • Closed

                Activity

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                pkulzer Paige Kulzer (Inactive) added a comment -

                Here are some sample VCF files that you could possibly test with: https://bioinformaticstools.mayo.edu/research/vcf-miner-sample-vcfs/

                Files with the ".gz" suffix will need to be gunzipped, for example:

                gunzip HG00098.anno.vcf.gz

                I would recommend starting with the smallest files since these VCF files can get quite large and complicated!

                Show
                pkulzer Paige Kulzer (Inactive) added a comment - Here are some sample VCF files that you could possibly test with: https://bioinformaticstools.mayo.edu/research/vcf-miner-sample-vcfs/ Files with the ".gz" suffix will need to be gunzipped, for example: gunzip HG00098.anno.vcf.gz I would recommend starting with the smallest files since these VCF files can get quite large and complicated!
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                nfreese Nowlan Freese added a comment -

                Work for this ticket was done in IGBF-4106.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Work for this ticket was done in IGBF-4106 . Closing ticket.

                  People

                  • Assignee:
                    sjagarap saideepthi jagarapu (Inactive)
                    Reporter:
                    sjagarap saideepthi jagarapu (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: