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  1. IGB
  2. IGBF-4002

Fix GFF null pointer exception when FASTA included

        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: I've noticed an occasional error in the logs when loading GFF files in IGB. It's not currently well-understood how GFF files are being parsed in IGB which is making the debugging process for this issue difficult.

          Task: Reproduce the error by following the instructions below, then investigate the IGB codebase to determine what's supposed to happen when a GFF file is parsed and loaded in IGB. For example, is the "##FASTA" section in a GFF file supposed to be parsed as the reference sequence when no genome is loaded in IGB? Please report your findings on this ticket.

          1. Open IGB
          2. Download prodigal_Lambda_phage_sequences.gff from Google Drive (may need permission - https://drive.google.com/drive/folders/14noPsmKYMxX9jgHYQhkjqaTGzT8z8bSK?usp=drive_link)
          3. Without selecting a genome, drag and drop prodigal_Lambda_phage_sequences.gff into IGB.

          Note: Files for testing are also available via the Loraine Lab Google Drive: https://drive.google.com/drive/folders/1MLsVItXNcskfiCAg62GFmxWc1-NR40Tx?usp=drive_link

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-4362 Fix GFF loading with multiple FASTA sequences

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

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-4029 Investigate GFF file from NCBI not loading in IGB

              • Major - Major loss of function.
              • To-Do

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3927 Investigate: GFF parser error

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

                Activity

                  People

                  • Assignee:
                    sjagarap saideepthi jagarapu (Inactive)
                    Reporter:
                    pkulzer Paige Kulzer
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                    Dates

                    • Created:
                      Updated:
                      Resolved: