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  1. IGB
  2. IGBF-1443

Implement Depth Graph (Soft-clip)

    Details

    • Type: New Feature
    • Status: Closed (View Workflow)
    • Priority: Minor
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      2.5
    • Sprint:
      Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep

      Description

      The track operation Depth Graph (All) is used to summarize the depth of reads. It does not include soft-clipped parts of the read.

      Add Depth Graph (Soft-clip) as a track operation for bam/sam. This would create a depth graph for just soft-clip parts of reads.

      This should be possible to do by copying how Depth Graph (All) functions, but using only syms of instance BamSoftChildSingletonSeqSym.

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            Hide
            nfreese Nowlan Freese added a comment - - edited

            Tested Supreeth's branch on Mac with files from GIAB and the test softclip files in Dropbox.

            Depth Graph (Soft-clip All) works correctly for all tested BAM/SAM files.
            Depth Graph (Soft-clip All) option only shows for BAM/SAM files (this is the correct behavior, as only BAM/SAM will have softclips).

            Code is similar to existing depth graph all code, but is separate so should not interfere.

            Recommend pull request Sai Supreeth Segu.

            Show
            nfreese Nowlan Freese added a comment - - edited Tested Supreeth's branch on Mac with files from GIAB and the test softclip files in Dropbox. Depth Graph (Soft-clip All) works correctly for all tested BAM/SAM files. Depth Graph (Soft-clip All) option only shows for BAM/SAM files (this is the correct behavior, as only BAM/SAM will have softclips). Code is similar to existing depth graph all code, but is separate so should not interfere. Recommend pull request Sai Supreeth Segu .
            Hide
            ssegu Sai Supreeth Segu added a comment -
            Show
            ssegu Sai Supreeth Segu added a comment - Created pull request. Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/826/igbf-1443
            Hide
            nfreese Nowlan Freese added a comment -

            Ann Loraine if you could please review the pull request.

            Show
            nfreese Nowlan Freese added a comment - Ann Loraine if you could please review the pull request.
            Hide
            aloraine Ann Loraine added a comment - - edited

            Merged. Master branch installers are available and ready for testing.

            Show
            aloraine Ann Loraine added a comment - - edited Merged. Master branch installers are available and ready for testing.
            Hide
            nfreese Nowlan Freese added a comment -

            Tested master dmg installer for Mac.

            Depth Graph (Soft-clip All) working correctly.

            Closing issue.

            Show
            nfreese Nowlan Freese added a comment - Tested master dmg installer for Mac. Depth Graph (Soft-clip All) working correctly. Closing issue.

              People

              • Assignee:
                ssegu Sai Supreeth Segu
                Reporter:
                nfreese Nowlan Freese
              • Votes:
                0 Vote for this issue
                Watchers:
                4 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: