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  1. IGB
  2. IGBF-2269

Use bam header to sort 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:
          5
        • Epic Link:
        • Sprint:
          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

          Description

          Situation: Because the bai file does not include the chromosome information, we have been assuming that the order of the bai file chromosomes are the same as that in IGB. However, many bai files are not ordered exactly the same as IGB. The only way to know for sure the order of the bai file is to look at the header of the bam file. However, because we allow the user to load a bai file directly, there may not be a readable bam file.

          Task: If a bam header was retrieved successfully, use the chromosome order from the bam header instead of the genome.txt order to assign chromosome values to the bai data. For example, if the order in the bam header is chr3, chr1, chr2, then this is the order that the data will be retrieved from the bai file. You do not need to sort the data.

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              is blocked by

              Task - A task that needs to be done. IGBF-2220 Check for bam header

              • Major - Major loss of function.
              • Closed
              relates to

              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
                4 older comments
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                nfreese Nowlan Freese added a comment - - edited

                Test URL:
                https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/chr1_3_2.bam.bai
                https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/chr1_3_2.bam

                http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Bam/Bam_HomoSapien.bai
                http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Bam/Bam_HomoSapien.bam

                ONLY the bai file (no bam file in same location)
                https://data.cyverse.org/dav-anon/iplant/home/nowlanf/testThree/chr1_3_2.bam.bai

                Show
                nfreese Nowlan Freese added a comment - - edited Test URL: https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/chr1_3_2.bam.bai https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/chr1_3_2.bam http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Bam/Bam_HomoSapien.bai http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Bam/Bam_HomoSapien.bam ONLY the bai file (no bam file in same location) https://data.cyverse.org/dav-anon/iplant/home/nowlanf/testThree/chr1_3_2.bam.bai
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                nfreese Nowlan Freese added a comment -

                Checking span for null allows the bai file to load via URL and if the bam file is not located within the same directory locally.

                When the bai file is located in the same directory as the bam file and loaded via URL, it is not loaded correctly, most likely due to the bam file not being found. Pawan is aware of this issue and is working on it.

                Recommend checking span is null and fixing issue with bam not found in URL.

                Show
                nfreese Nowlan Freese added a comment - Checking span for null allows the bai file to load via URL and if the bam file is not located within the same directory locally. When the bai file is located in the same directory as the bam file and loaded via URL, it is not loaded correctly, most likely due to the bam file not being found. Pawan is aware of this issue and is working on it. Recommend checking span is null and fixing issue with bam not found in URL.
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                pbole Pawan Bole (Inactive) added a comment -

                https://bitbucket.org/pawanbole/integrated-genome-browser-pawan/commits/3945d1a325f8a8cca61b042787243750ecc45d71?at=IGBF-2269

                Pushed the changes related for the files present on the internet and also handled the missing null checks.

                Show
                pbole Pawan Bole (Inactive) added a comment - https://bitbucket.org/pawanbole/integrated-genome-browser-pawan/commits/3945d1a325f8a8cca61b042787243750ecc45d71?at=IGBF-2269 Pushed the changes related for the files present on the internet and also handled the missing null checks.
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                nfreese Nowlan Freese added a comment -

                Loading the bai file via url works correctly with or without the bam file in the same directory.

                Loading the bai file locally works correctly with or without the bam file in the same directory.

                Recommend pull request.

                Show
                nfreese Nowlan Freese added a comment - Loading the bai file via url works correctly with or without the bam file in the same directory. Loading the bai file locally works correctly with or without the bam file in the same directory. Recommend pull request.
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                pbole Pawan Bole (Inactive) added a comment -

                Nowlan Freese
                Pull request generated.
                https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/776/igbf-2269/diff

                Show
                pbole Pawan Bole (Inactive) added a comment - Nowlan Freese Pull request generated. https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/776/igbf-2269/diff

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: