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  1. IGB
  2. IGBF-2647

Soft Clip Depth Graph incorrect for PacBio files

        Details

        • Type: Bug
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 4 2021 May 3 - May 14

          Description

          Situation: The Depth Graph (Soft-clip All) track operation on PacBio data is providing incorrect results.

          To replicate:
          Load the H_sapiens_Dec_2013 genome.
          Add the attached sonAshMinimap2_1LINE.bam file.
          Navigate to chr1:10,643,151-10,643,319
          Click load data.
          Right-click on the bam file track label and select Track Operations > Depth Graph (Soft-clip All).
          Note that there is one soft clip at the beginning of the read, but the graph states there are approximately 800 soft clips.

          Task: Fix the Depth Graph (Soft-clip All) operator so that it displays the correct soft-clip depth information for PacBio files.

            Attachments

              Issue Links

              relates to

              New Feature - A new feature of the product, which has yet to be developed. IGBF-1443 Implement Depth Graph (Soft-clip)

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

              Task - A task that needs to be done. IGBF-2627 Test Soft-Clipping Subsystem - MacOS

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-2593 [ 18777 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2627 [ IGBF-2627 ]
                nfreese Nowlan Freese made changes -
                Description Situation: The soft-clipping depth graph (All) operator on PacBio data is providing incorrect results.

                To replicate: Load the

                Task: Fix the soft-clip depth graph (All) operator so that it displays the correct soft-clip depth information.                 		Situation: The Depth Graph (Soft-clip All) track operation on PacBio data is providing incorrect results.

                To replicate:
                Load the H_sapiens_Dec_2013 genome.
                Load the attached sonAshMinimap2_1LINE.bam file.
                Navigate to chr1:10,643,151-10,643,319
                Right-click on the bam file track label and select Track Operations > Depth Graph (Soft-clip All)

                Task: Fix the soft-clip depth graph (All) operator so that it displays the correct soft-clip depth information.
                nfreese Nowlan Freese made changes -
                Description Situation: The Depth Graph (Soft-clip All) track operation on PacBio data is providing incorrect results.

                To replicate:
                Load the H_sapiens_Dec_2013 genome.
                Load the attached sonAshMinimap2_1LINE.bam file.
                Navigate to chr1:10,643,151-10,643,319
                Right-click on the bam file track label and select Track Operations > Depth Graph (Soft-clip All)

                Task: Fix the soft-clip depth graph (All) operator so that it displays the correct soft-clip depth information.                 		Situation: The Depth Graph (Soft-clip All) track operation on PacBio data is providing incorrect results.

                To replicate:
                Load the H_sapiens_Dec_2013 genome.
                Add the attached sonAshMinimap2_1LINE.bam file.
                Navigate to chr1:10,643,151-10,643,319
                Click load data.
                Right-click on the bam file track label and select Track Operations > Depth Graph (Soft-clip All).
                Note that there is one soft clip at the beginning of the read, but the graph states there are approximately 800 soft clips.

                Task: Fix the Depth Graph (Soft-clip All) operator so that it displays the correct soft-clip depth information for PacBio files.
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-1443 [ IGBF-1443 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Epic Link IGBF-2593 [ 18777 ] IGBF-1765 [ 17855 ]
                nfreese Nowlan Freese made changes -
                Sprint Fall 5 Nov 9 - Nov 20 [ 108 ] Fall 6 Nov 23 - Dec 4 [ 109 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] 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 ]
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Assignee Sai Supreeth Segu [ ssegu ]
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ssegu Sai Supreeth Segu (Inactive) made changes -
                Assignee Sai Supreeth Segu [ ssegu ] Ann Loraine [ aloraine ]
                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 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 6 Nov 23 - Dec 4 [ 109 ] Fall 5 Nov 9 - Nov 20 [ 108 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20 [ 108 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 23 - Dec 4 [ 108, 109 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11 [ 108, 109 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 108, 109, 110 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 108, 109, 110 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 108, 109, 110, 111 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 108, 109, 110, 111 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 108, 109, 110, 111, 112 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 108, 109, 110, 111, 112 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 108, 109, 110, 111, 112, 113 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 108, 109, 110, 111, 112, 113 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 108, 109, 110, 111, 112, 113, 114 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 108, 109, 110, 111, 112, 113, 114 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 108, 109, 110, 111, 112, 113, 114, 115 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 108, 109, 110, 111, 112, 113, 114, 115 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19 [ 108, 109, 110, 111, 112, 113, 114, 116 ]
                ann.loraine Ann Loraine made changes -
                Assignee Irvin Naylor [ inaylor ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                inaylor Irvin Naylor (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                inaylor Irvin Naylor (Inactive) made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                inaylor Irvin Naylor (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19 [ 108, 109, 110, 111, 112, 113, 114, 116 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 1 Mar 22 - Apr 2 [ 108, 109, 110, 111, 112, 113, 114, 116, 117 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                inaylor Irvin Naylor (Inactive) made changes -
                Attachment 2647_1.PNG [ 15552 ]
                Attachment 2647_2.PNG [ 15553 ]
                nfreese Nowlan Freese made changes -
                Attachment soft-match-deletion-match-insertion-match-soft_8.sam [ 15555 ]
                Attachment soft-match-deletion-match-insertion-match-soft.sam [ 15556 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                inaylor Irvin Naylor (Inactive) made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Irvin Naylor [ inaylor ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2 [ 108, 109, 110, 111, 112, 113, 114, 116, 117 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19 [ 108, 109, 110, 111, 112, 113, 114, 116 ]
                inaylor Irvin Naylor (Inactive) made changes -
                Assignee Irvin Naylor [ inaylor ]
                inaylor Irvin Naylor (Inactive) made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19 [ 108, 109, 110, 111, 112, 113, 114, 116 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 4 2021 May 3 - May 14 [ 108, 109, 110, 111, 112, 113, 114, 116, 120 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 4 2021 May 3 - May 14 [ 108, 109, 110, 111, 112, 113, 114, 116, 120 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28 [ 108, 109, 110, 111, 112, 113, 114, 116, 120, 121 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28 [ 108, 109, 110, 111, 112, 113, 114, 116, 120, 121 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 4 2021 May 3 - May 14 [ 108, 109, 110, 111, 112, 113, 114, 116, 120 ]
                inaylor Irvin Naylor (Inactive) made changes -
                Assignee Irvin Naylor [ inaylor ]

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    nfreese Nowlan Freese
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                    Watchers:
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                    Dates

                    • Created:
                      Updated: