Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-4411

Add more SAMtags to SAMtags filter function

    Details

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

      Attachments

        Issue Links

          Activity

          Show
          karthik Karthik Raveendran added a comment - - edited See Commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/branch/IGBF-4411 PR Submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1102
          Hide
          karthik Karthik Raveendran added a comment - - edited

          SAMtags should be in alphabetical order which has been implemented in commit
          PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1103

          Show
          karthik Karthik Raveendran added a comment - - edited SAMtags should be in alphabetical order which has been implemented in commit PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1103
          Show
          karthik Karthik Raveendran added a comment - Added 83 SAMtags: commit PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1104
          Hide
          karthik Karthik Raveendran added a comment -
          Show
          karthik Karthik Raveendran added a comment - Made SAMtags filter dropdown editable. See commit PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1104
          Hide
          karthik Karthik Raveendran added a comment -
          Show
          karthik Karthik Raveendran added a comment - PR is updated with squashed commits: PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1104
          Hide
          ann.loraine Ann Loraine added a comment -

          PR is merged.

          Show
          ann.loraine Ann Loraine added a comment - PR is merged.
          Hide
          ann.loraine Ann Loraine added a comment -

          Build failed, but probably not due to Karthik Raveendran's changes. The failure happens during a test. Re-running the pipeline.

          Show
          ann.loraine Ann Loraine added a comment - Build failed, but probably not due to Karthik Raveendran 's changes. The failure happens during a test. Re-running the pipeline.
          Hide
          ann.loraine Ann Loraine added a comment -

          Issue was fixed as part of IGBF-4412.
          Installers are now built and deployed to "early access" section of bioviz.org.
          Ready for testing.

          Show
          ann.loraine Ann Loraine added a comment - Issue was fixed as part of IGBF-4412 . Installers are now built and deployed to "early access" section of bioviz.org. Ready for testing.
          Hide
          karthik Karthik Raveendran added a comment -

          Null point exception found for Color by because arraylist initialization was accidently deleted when the changes to the code was made. This issue is fixed in the new commit
          PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1106

          Show
          karthik Karthik Raveendran added a comment - Null point exception found for Color by because arraylist initialization was accidently deleted when the changes to the code was made. This issue is fixed in the new commit PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1106
          Hide
          ann.loraine Ann Loraine added a comment -

          PR is merged and new installers are built and deployed to bioviz.org early access section. Ready for testing.

          Show
          ann.loraine Ann Loraine added a comment - PR is merged and new installers are built and deployed to bioviz.org early access section. Ready for testing.
          Hide
          karthik Karthik Raveendran added a comment -

          Issue with NH value comparison: The value needed to be string before it can be compared and filtered - so number will not work. Fixed in commit

          Show
          karthik Karthik Raveendran added a comment - Issue with NH value comparison: The value needed to be string before it can be compared and filtered - so number will not work. Fixed in commit
          Show
          karthik Karthik Raveendran added a comment - PR Submitted https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1108
          Hide
          karthik Karthik Raveendran added a comment -

          Fix the code to make filter case sensitivity. See commit

          Show
          karthik Karthik Raveendran added a comment - Fix the code to make filter case sensitivity. See commit
          Hide
          ann.loraine Ann Loraine added a comment -

          Thank you Karthik Raveendran!

          PR is merged and pipeline launched to build "installers for dev".

          Show
          ann.loraine Ann Loraine added a comment - Thank you Karthik Raveendran ! PR is merged and pipeline launched to build "installers for dev".
          Hide
          ann.loraine Ann Loraine added a comment -

          Installers are built and deployed to bioviz.org early access section. Ready for final testing.

          Show
          ann.loraine Ann Loraine added a comment - Installers are built and deployed to bioviz.org early access section. Ready for final testing.
          Hide
          nfreese Nowlan Freese added a comment -

          Testing installer on Mac.

          • Color By SAMtag "AS" works with value of 90.
          • Color By typed in value "CIGAR" works with value of 5M286N85M
          • Filter By SAMtag "AS" works with value of 90 for equals or does not equal.
          • Filter By SAMtag "CY" works with value of FFFFFFFFFFFFFF,F for equals or does not equal.
          • Filter By SAMtag "CB" is case sensitive for a value of ATCACTTAGAGAGaAC-1

          No errors in the logs.

          Closing ticket.

          Show
          nfreese Nowlan Freese added a comment - Testing installer on Mac. Color By SAMtag "AS" works with value of 90. Color By typed in value "CIGAR" works with value of 5M286N85M Filter By SAMtag "AS" works with value of 90 for equals or does not equal. Filter By SAMtag "CY" works with value of FFFFFFFFFFFFFF,F for equals or does not equal. Filter By SAMtag "CB" is case sensitive for a value of ATCACTTAGAGAGaAC-1 No errors in the logs. Closing ticket.

            People

            • Assignee:
              karthik Karthik Raveendran
              Reporter:
              karthik Karthik Raveendran
            • Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: