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  1. IGB
  2. IGBF-1441

Fix Depth Graph (Start) Soft-clip coordinates

        Details

        • Story Points:
          2
        • Sprint:
          Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3, Spring 2019 Sprint 1

          Description

          Depth graph track operations are used to add up the amount of read depth from bam/sam files. The soft-clipped portion of a read should not count towards either Depth Graph (Start) or Depth Graph (All).

          Currently Depth Graph (All) does not include the soft-clipped portion (correct). However, Depth Graph (Start) does count the soft-clipped portion (bug).

          Example soft-clip files can be found in Dropbox > IGB > Jira Issues > IGBF-1291 Soft-Clip > exampleFiles

          Potential classes worth investigating:
          SeqSymSummarizer > getSpanStartSummary
          Delegate - getRegion

            Attachments

            1. example.bed
              0.1 kB
            2. GFF3_example_1_EDITED_negative.gff3
              0.8 kB
            3. GFF3_example_1_EDITED.gff3
              0.8 kB
            4. IGBF1441_Review_Screenshot.PNG
              IGBF1441_Review_Screenshot.PNG
              205 kB
            5. IGBF1441_Testing.docx
              603 kB
            6. onlyMatchesNegativeShifted.sam
              0.1 kB
            7. onlyMatchesShifted-2.sam
              0.2 kB
            8. softClip-depthGraphStart.png
              softClip-depthGraphStart.png
              79 kB
            9. softClip-DepthGraphStart-CORRECT.png
              softClip-DepthGraphStart-CORRECT.png
              109 kB
            10. softClipShifted2.sam
              0.2 kB
            11. soft-match-deletion-match-insertion-match-soft.sam
              0.1 kB
            12. VCF_HomoSapien_EDITED.vcf
              1 kB

              Issue Links

              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1291 Show soft-clipped bases in BAM files

              • Major - Major loss of function.
              • Closed

                Activity

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                8 older comments
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                nfreese Nowlan Freese added a comment -

                Need testing on my current branch to see if the GFF3 files are now working correctly.

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                nfreese Nowlan Freese added a comment - Need testing on my current branch to see if the GFF3 files are now working correctly.
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                srishteeM Srishtee Marotkar (Inactive) added a comment - - edited

                Please Check 'IGBF1441_Review_Screenshot' attached file.

                Downloaded installer from https://bitbucket.org/nfreese/nowlanfork-igb/downloads/ with name 'IGB-IGBF-1441-SoftclipDepthGraphStartBug-x64.exe' and it is now showing Depth Graph(Start) for GFF3 files loaded from smoking test data

                Show
                srishteeM Srishtee Marotkar (Inactive) added a comment - - edited Please Check 'IGBF1441_Review_Screenshot' attached file. Downloaded installer from https://bitbucket.org/nfreese/nowlanfork-igb/downloads/ with name 'IGB- IGBF-1441 -SoftclipDepthGraphStartBug-x64.exe' and it is now showing Depth Graph(Start) for GFF3 files loaded from smoking test data
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                nfreese Nowlan Freese added a comment -

                Testing Mac: Working Correctly

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                nfreese Nowlan Freese added a comment - Testing Mac: Working Correctly
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                svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment -

                Linux testing successful

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                svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - Linux testing successful
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                svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment -

                Testing Windows: Working Correctly

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                svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - Testing Windows: Working Correctly

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
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                    Watchers:
                    5 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: