Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3903

Add CRAM file format to the release testing documentation

    Details

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

      Description

      Situation: We've recently added support for the CRAM file format to IGB.

      Task: Update the File Formats page of the IGB Release Documentation to include a test case for the CRAM file format.

        Attachments

          Activity

          pkulzer Paige Kulzer created issue -
          pkulzer Paige Kulzer made changes -
          Field Original Value New Value
          Epic Link IGBF-1531 [ 17617 ]
          pkulzer Paige Kulzer made changes -
          Rank Ranked higher
          pkulzer Paige Kulzer made changes -
          Status To-Do [ 10305 ] In Progress [ 3 ]
          pkulzer Paige Kulzer made changes -
          Attachment NB72462M_HomoSapien.cram [ 18502 ]
          pkulzer Paige Kulzer made changes -
          Attachment NB72462M_HomoSapien.cram.crai [ 18503 ]
          Hide
          pkulzer Paige Kulzer added a comment -

          I've added a CRAM section to the File Formats page which includes the name of the file to be added from the Smoke Testing Quickload, the chromosome and region to zoom to, and a picture of what IGB should look like at that region.

          Next steps: Add the CRAM file and its index to the Smoke Testing Quickload. Since the original CRAM file is quite large, I've subsetted it to only include a small region of chromosome 2 using samtools:

          samtools view -Cho NB72462M_HomoSapien.cram NB72462M.cram chr2:124,477,335-124,477,438
          samtools index NB72462M_HomoSapien.cram 
          

          I then checked the header to confirm that only the specified region was included (which it was):

          samtools view -H NB72462M_HomoSapien.cram 
          
          Show
          pkulzer Paige Kulzer added a comment - I've added a CRAM section to the File Formats page which includes the name of the file to be added from the Smoke Testing Quickload, the chromosome and region to zoom to, and a picture of what IGB should look like at that region. Next steps: Add the CRAM file and its index to the Smoke Testing Quickload. Since the original CRAM file is quite large, I've subsetted it to only include a small region of chromosome 2 using samtools: samtools view -Cho NB72462M_HomoSapien.cram NB72462M.cram chr2:124,477,335-124,477,438 samtools index NB72462M_HomoSapien.cram I then checked the header to confirm that only the specified region was included (which it was): samtools view -H NB72462M_HomoSapien.cram
          pkulzer Paige Kulzer made changes -
          Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
          pkulzer Paige Kulzer made changes -
          Assignee Paige Kulzer [ pkulzer ] Nowlan Freese [ nfreese ]
          nfreese Nowlan Freese made changes -
          Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
          Hide
          nfreese Nowlan Freese added a comment - - edited

          The testing documentation looks good, and I was able to view the CRAM file.

          I have deployed the Cram file to the smoketesting S3 bucket used for release testing here: https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/

          Closing ticket

          Show
          nfreese Nowlan Freese added a comment - - edited The testing documentation looks good, and I was able to view the CRAM file. I have deployed the Cram file to the smoketesting S3 bucket used for release testing here: https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/ Closing ticket
          nfreese Nowlan Freese made changes -
          Assignee Nowlan Freese [ nfreese ] Paige Kulzer [ pkulzer ]
          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 ]

            People

            • Assignee:
              pkulzer Paige Kulzer
              Reporter:
              pkulzer Paige Kulzer
            • Votes:
              0 Vote for this issue
              Watchers:
              Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: