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  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

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            is blocked by

            Bug - A problem which impairs or prevents the functions of the product. IGBF-4412 Fix issue with DAS test

            • Major - Major loss of function.
            • Closed

              Activity

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              karthik Karthik Raveendran created issue -
              karthik Karthik Raveendran made changes -
              Field Original Value New Value
              Epic Link IGBF-3765 [ 22984 ]
              karthik Karthik Raveendran made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              karthik Karthik Raveendran made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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              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

              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
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              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
              karthik Karthik Raveendran made changes -
              Assignee Karthik Raveendran [ karthik ] Ann Loraine [ aloraine ]
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              karthik Karthik Raveendran added a comment -

              Added 83 SAMtags: commit
              PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1104

              Show
              karthik Karthik Raveendran added a comment - Added 83 SAMtags: commit PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1104
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              karthik Karthik Raveendran added a comment -

              Made SAMtags filter dropdown editable. See commit
              PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1104

              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
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              karthik Karthik Raveendran added a comment -

              PR is updated with squashed commits:
              PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1104

              Show
              karthik Karthik Raveendran added a comment - PR is updated with squashed commits: PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1104
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              ann.loraine Ann Loraine added a comment -

              PR is merged.

              Show
              ann.loraine Ann Loraine added a comment - PR is merged.
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              ann.loraine Ann Loraine made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
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              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.
              nfreese Nowlan Freese made changes -
              Link This issue is blocked by IGBF-4412 [ IGBF-4412 ]
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              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.
              ann.loraine Ann Loraine made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              karthik Karthik Raveendran made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              karthik Karthik Raveendran made changes -
              Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
              karthik Karthik Raveendran made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
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              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
              karthik Karthik Raveendran made changes -
              Assignee Nowlan Freese [ nfreese ]
              karthik Karthik Raveendran made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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              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.
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              ann.loraine Ann Loraine made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              ann.loraine Ann Loraine made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              Hide
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              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
              karthik Karthik Raveendran made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              karthik Karthik Raveendran made changes -
              Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
              karthik Karthik Raveendran made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              karthik Karthik Raveendran made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              Hide
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              karthik Karthik Raveendran added a comment -

              PR Submitted https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1108

              Show
              karthik Karthik Raveendran added a comment - PR Submitted https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1108
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              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
              karthik Karthik Raveendran made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              karthik Karthik Raveendran made changes -
              Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
              karthik Karthik Raveendran made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              karthik Karthik Raveendran made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              Hide
              Permalink
              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
              Permalink
              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.
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              ann.loraine Ann Loraine made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              ann.loraine Ann Loraine made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              Hide
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              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.
              nfreese Nowlan Freese made changes -
              Assignee Nowlan Freese [ nfreese ] Karthik Raveendran [ karthik ]
              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:
                  karthik Karthik Raveendran
                  Reporter:
                  karthik Karthik Raveendran
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                  0 Vote for this issue
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                  Dates

                  • Created:
                    Updated:
                    Resolved: