Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2100

Scale Bai Data

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          2
        • Epic Link:
        • 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

            Attachments

              Issue Links

              relates to

              Story - Created by JIRA Software - do not edit or delete. Issue type for a user story. IGBF-1920 Visualizing the index

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                Hide
                Permalink
                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Bai.java has been renamed to BaiToBedgraphConverter.java

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

                Pull request submitted.

                Show
                svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - Pull request submitted.
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/761/scale-bai-data-remove-negetive-values-in/diff

                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
                Permalink
                ann.loraine 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
                ann.loraine 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
                Permalink
                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 (Inactive)
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    4 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: