Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3478

Add CRAM support to IGB

        Details

        • Story Points:
          5
        • Epic Link:
        • Sprint:
          Fall 4 2023 Oct 16, Fall 6, Fall 7, Fall 8, Spring 1, Spring 2

          Description

          Task: Add CRAM file support to IGB.

          Task list:

          • Implement CRAM reference source
          • Implement CRAM file type handler
          • Implement CRAM methods(parse(), getSAMReader())
          • Load 2-bit data from code
          • Check the possibility of unit tests
          • Review the code
          • Test code with different input samples

          Working Branch

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3550 Add CRAM to list of supported files for BioViz Connect

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

              Task - A task that needs to be done. IGBF-3464 Deploy htsjdk-igb

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3465 Update BigWig/BigBed htsjdk-igb version

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

              Task - A task that needs to be done. IGBF-3543 Rebase cram changes on main-JDK21-with-javafx-no-theme

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                9 older comments
                Hide
                Permalink
                kgopu Kaushik Gopu added a comment -

                Notes on discussion with Nowlan Freese:

                • HTSJDK downloads the entire sequence before decoding the records. This sequence is loaded once and will be available for the entire session.
                • The HTSJDK team does not yet implement a loading sequence based on the chromosome range.
                • Tested loading strategy for CRAM in IGV. Since IGV uses the HTSJDK library, the complete sequence is loaded for CRAM.
                Show
                kgopu Kaushik Gopu added a comment - Notes on discussion with Nowlan Freese : HTSJDK downloads the entire sequence before decoding the records. This sequence is loaded once and will be available for the entire session. The HTSJDK team does not yet implement a loading sequence based on the chromosome range. Tested loading strategy for CRAM in IGV. Since IGV uses the HTSJDK library, the complete sequence is loaded for CRAM.
                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited

                Testing on Mac:

                • Tested loading various cram files locally for the A thaliana genome (see Google Drive).
                • Tested loading a cram file via URL.
                • Tested loading an incompatible cram file and seeing the MD5 error (A_thaliana_Jun_2009_Chr1_3regions_IGV-works.cram).

                Everything appears to be working as expected. The sequence is being loaded for the entire length of data on the viewed chromosome, regardless of how zoomed in the user is (this is what we decided would work best for now). Caching the genome appears to be working correctly.

                Show
                nfreese Nowlan Freese added a comment - - edited Testing on Mac: Tested loading various cram files locally for the A thaliana genome (see Google Drive ). Tested loading a cram file via URL . Tested loading an incompatible cram file and seeing the MD5 error (A_thaliana_Jun_2009_Chr1_3regions_IGV-works.cram). Everything appears to be working as expected. The sequence is being loaded for the entire length of data on the viewed chromosome, regardless of how zoomed in the user is (this is what we decided would work best for now). Caching the genome appears to be working correctly.
                Hide
                Permalink
                kgopu Kaushik Gopu added a comment - - edited

                main-JDK8 - Pull Request has been submitted.

                Show
                kgopu Kaushik Gopu added a comment - - edited main-JDK8 - Pull Request has been submitted.
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                PR is merged. Branch installers are built and ready for download and testing at:

                https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/

                Note: Branch installer file names contain prefix "main-JDK8" as the merge target was the main-JDK8 branch.

                Show
                ann.loraine Ann Loraine added a comment - - edited PR is merged. Branch installers are built and ready for download and testing at: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/ Note: Branch installer file names contain prefix "main-JDK8" as the merge target was the main-JDK8 branch.
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Tested installer on Mac.
                Able to load cram files locally and via URL, and able to see the MD5 error when there is an issue with the cram.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested installer on Mac. Able to load cram files locally and via URL, and able to see the MD5 error when there is an issue with the cram. Closing ticket.

                  People

                  • Assignee:
                    kgopu Kaushik Gopu
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: