Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Story Points:
      2
    • Sprint:
      Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec, Fall 9 : 9 Dec to 20 Dec

      Description

      Situation:
      When determining the offsets between each level 5 region of the BAI file, the output is the number of bytes/bits. Depending on the size of the BAM file, these numbers can be very large. The data should be scaled for easier viewing in IGB.

      In addition, some of the offsets are negative. It is unclear why they are negative, but when we compare the negatives to estimateCoverage from BioVizBase, they are always set to 0.

      Task:
      Set any negative offsets to 0.

      Scale the data by determining either the mean or median for all offsets across the BAI file, then divide the offsets by that number. This should result in most offset values being around 1.

      Look at Bai.java

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            Hide
            stiwari8 Srishti Tiwari added a comment -

            Bai.java has been renamed to BaiToBedgraphConverter.java

            Show
            stiwari8 Srishti Tiwari added a comment - Bai.java has been renamed to BaiToBedgraphConverter.java
            Hide
            svallapu Sai Charan Reddy Vallapureddy added a comment - - edited

            Nowlan Freese
            Branch: https://bitbucket.org/svallapu/charan_igb/branch/IGBF-2100-New

            Tasks:
            1. Removed Negative values. It scaled the bed graph.
            2. Last chuck is now handled.

            Note: Logic for generating graph is changed. (More lines are added and removed for the same)

            Show
            svallapu Sai Charan Reddy Vallapureddy added a comment - - edited Nowlan Freese Branch: https://bitbucket.org/svallapu/charan_igb/branch/IGBF-2100-New Tasks: 1. Removed Negative values. It scaled the bed graph. 2. Last chuck is now handled. Note: Logic for generating graph is changed. (More lines are added and removed for the same)
            Hide
            nfreese Nowlan Freese added a comment -

            Data is scaled correctly and negative values are now set at 0. In addition, the final chunk of each chromosome is showing correctly.

            Ready for pull request.

            Show
            nfreese Nowlan Freese added a comment - Data is scaled correctly and negative values are now set at 0. In addition, the final chunk of each chromosome is showing correctly. Ready for pull request.
            Hide
            svallapu Sai Charan Reddy Vallapureddy added a comment -

            Pull request submitted.

            Show
            svallapu Sai Charan Reddy Vallapureddy added a comment - Pull request submitted.
            Show
            nfreese Nowlan Freese added a comment - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/761/scale-bai-data-remove-negetive-values-in/diff
            Hide
            aloraine Ann Loraine added a comment -

            Merged to master.

            Sai Charan Reddy Vallapureddy and Nowlan Freese - please note I am about to increment master branch to 9.1.2. You may wish to wait until those for testing.

            Show
            aloraine Ann Loraine added a comment - Merged to master. Sai Charan Reddy Vallapureddy and Nowlan Freese - please note I am about to increment master branch to 9.1.2. You may wish to wait until those for testing.
            Hide
            nfreese Nowlan Freese added a comment -

            Data are scaled with no negative values. Last chunk is present.

            Closing issue.

            Show
            nfreese Nowlan Freese added a comment - Data are scaled with no negative values. Last chunk is present. Closing issue.

              People

              • Assignee:
                svallapu Sai Charan Reddy Vallapureddy
                Reporter:
                nfreese Nowlan Freese
              • Votes:
                0 Vote for this issue
                Watchers:
                4 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: