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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

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                sjagarap saideepthi jagarapu (Inactive) added a comment -

                Investigated parsing logic in both IGB and IGV in linked tickets IGBF-4082, IGBF-4083

                First step would be trying to integrate htsjdk library to make the manual logic of VCF parsing to use in-built parser in IGB.

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                sjagarap saideepthi jagarapu (Inactive) added a comment - Investigated parsing logic in both IGB and IGV in linked tickets IGBF-4082 , IGBF-4083 First step would be trying to integrate htsjdk library to make the manual logic of VCF parsing to use in-built parser in IGB.
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                sjagarap saideepthi jagarapu (Inactive) added a comment -

                High-Level Implementation Overview

                1. VCF File Reading

                • Replaced manual LineReader with VCFFileReader
                • Using VCFHeader for proper header parsing

                2. Variant Processing

                • Removed LineProcessor dependency
                • Using VariantContext to handle variant details
                • Direct access to variant properties (position, alleles, filters)

                3. Filter and header Handling

                • Using VCFHeader for filter descriptions
                • Used variant functions like .getsamples() to extract sample, filter information instead of storing them in maps
                Show
                sjagarap saideepthi jagarapu (Inactive) added a comment - High-Level Implementation Overview 1. VCF File Reading Replaced manual LineReader with VCFFileReader Using VCFHeader for proper header parsing 2. Variant Processing Removed LineProcessor dependency Using VariantContext to handle variant details Direct access to variant properties (position, alleles, filters) 3. Filter and header Handling Using VCFHeader for filter descriptions Used variant functions like .getsamples() to extract sample, filter information instead of storing them in maps
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                sjagarap saideepthi jagarapu (Inactive) added a comment - - edited

                Code changes branch : https://bitbucket.org/lorainelab-deepthi/integrated-genome-browser/branch/IGBF-4106

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                sjagarap saideepthi jagarapu (Inactive) added a comment - - edited Code changes branch : https://bitbucket.org/lorainelab-deepthi/integrated-genome-browser/branch/IGBF-4106
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                nfreese Nowlan Freese added a comment -

                Deepthi and I did a high level code review. Everything looks good and vcf files are loading. As we would like to do some additional testing, we have created a new ticket, IGBF-4166, to test multiple vcf files on the new code prior to merging it into main.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Deepthi and I did a high level code review. Everything looks good and vcf files are loading. As we would like to do some additional testing, we have created a new ticket, IGBF-4166 , to test multiple vcf files on the new code prior to merging it into main. Closing ticket.

                  People

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

                    • Created:
                      Updated:
                      Resolved: