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  1. IGB
  2. IGBF-2221

Compare bin sizes to chromosome sizes

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          5
        • Epic Link:
        • Sprint:
          Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul

          Description

          When loading a bai file, if no bam file or its header is found, compare the bin sizes of the bai file to the chromosome lengths for the selected genome. Use this comparison to determine the order of the chromosomes. For example if the bin sizes are 16kbp, 32kbp, 64kbp and the chromosome sizes are Chr1:15kbp, Chr2:61kbp, and Chr3:32kbp, the order of the bai file must be Chr1, Chr3, Chr2. Use this to correctly order the chromosomes in the bai graph in IGB.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2482 Refactor Index Hacking code

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2210 Investigate Index Hacking discrepancies

              • 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-1919 [ 18010 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2210 [ IGBF-2210 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan [ 85 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb [ 85, 86 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb [ 85, 86 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 21 Feb [ 85, 86, 87 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb [ 85, 86, 87 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 85, 86, 87, 89 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                pbole Pawan Bole (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pbole Pawan Bole (Inactive) made changes -
                Assignee Pawan Bole [ pbole ]
                pbole Pawan Bole (Inactive) made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 85, 86, 87, 89 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 85, 86, 87, 89, 90 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                pbole Pawan Bole (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 85, 86, 87, 89, 90 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 85, 86, 87, 89, 90, 91 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Attachment exampleOfWhatIndexFileLooksLike.txt [ 14687 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 85, 86, 87, 89, 90, 91 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 85, 86, 87, 89, 90, 91, 92 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 85, 86, 87, 89, 90, 91, 92 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 85, 86, 87, 89, 90, 91, 92, 93 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 85, 86, 87, 89, 90, 91, 92, 93 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 85, 86, 87, 89, 90, 91, 92, 93, 94 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pbole Pawan Bole (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pbole Pawan Bole (Inactive) made changes -
                Assignee Pawan Bole [ pbole ] Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 85, 86, 87, 89, 90, 91, 92, 93, 94 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 85, 86, 87, 89, 90, 91, 92, 93, 94, 95 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 85, 86, 87, 89, 90, 91, 92, 93, 94, 95 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun [ 85, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun [ 85, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 July [ 85, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96, 97 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul [ 85, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96, 97 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 3 Jul - 14 Jul [ 85, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                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 ] 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 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2482 [ IGBF-2482 ]

                  People

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

                    Dates

                    • Created:
                      Updated:
                      Resolved: