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  1. IGB
  2. IGBF-1098

Update BAM, tabix reader libraries

        Details

        • Story Points:
          1
        • Sprint:
          B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3

          Description

          We need to upgrade our sam/bam parsing library to be in line with the updated sam/bam specification. Currently some header flags which are part of the specification (i.e. SO) will cause exceptions to be thrown by the samtools libary and prevent the ability of users to load their data.

          We should update our libary and parsers to resolve the issue.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-1321 Test for errors due to htsjdk library update

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-1417 Create new artifact with bigbed and bigwig parsing code from IGV codebase

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1418 Import htsjdk as OSGi bundle

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1699 Remove unneeded dependencies from modules

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-1321 Test for errors due to htsjdk library update

              • Major - Major loss of function.
              • Closed

                Activity

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                17 older comments
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                kkorey Kiran Korey (Inactive) added a comment -

                You can find the tribble jar at the path : https://github.com/nh13/IGV/tree/master/lib
                Steps followed:
                Renamed the downloaded jar to tribble-ext-1.111 and replaced the existing jar in the local maven repository.
                Now IGB is new the new jar as tribble-ext and this is not dependent on net.sf.samtools, but it is dependent on the org.apache.log4j so we will need to add it as the library.

                Also if you want to look at the source code of this new jar please use Intellij.
                Look for Maven:org.broad:tribble-ext:1.111 and expand the arrow next to it.

                Using the new jar IGB loads the BigBed and BigWig without any error.

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                kkorey Kiran Korey (Inactive) added a comment - You can find the tribble jar at the path : https://github.com/nh13/IGV/tree/master/lib Steps followed: Renamed the downloaded jar to tribble-ext-1.111 and replaced the existing jar in the local maven repository. Now IGB is new the new jar as tribble-ext and this is not dependent on net.sf.samtools, but it is dependent on the org.apache.log4j so we will need to add it as the library. Also if you want to look at the source code of this new jar please use Intellij. Look for Maven:org.broad:tribble-ext:1.111 and expand the arrow next to it. Using the new jar IGB loads the BigBed and BigWig without any error.
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                ann.loraine Ann Loraine added a comment - - edited

                Please locate version control repository for tribble-ext artifacts so that we can fork the repository and build it as bundle natively.

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                ann.loraine Ann Loraine added a comment - - edited Please locate version control repository for tribble-ext artifacts so that we can fork the repository and build it as bundle natively.
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                kkorey Kiran Korey (Inactive) added a comment -

                This link has similar code to what tribble-ext has https://github.com/samtools/htsjdk/tree/master/src/main/java/htsjdk/tribble

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                kkorey Kiran Korey (Inactive) added a comment - This link has similar code to what tribble-ext has https://github.com/samtools/htsjdk/tree/master/src/main/java/htsjdk/tribble
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                ann.loraine Ann Loraine added a comment -

                We will create an htsjdk bundle and distribute to the project via https://nexus.bioviz.org. This issue is now replaced with https://jira.transvar.org/browse/IGBF-1418

                Show
                ann.loraine Ann Loraine added a comment - We will create an htsjdk bundle and distribute to the project via https://nexus.bioviz.org . This issue is now replaced with https://jira.transvar.org/browse/IGBF-1418
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                ann.loraine Ann Loraine added a comment -

                Closing this issue because strategy for reaching a solution has changed.

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                ann.loraine Ann Loraine added a comment - Closing this issue because strategy for reaching a solution has changed.

                  People

                  • Assignee:
                    kkorey Kiran Korey (Inactive)
                    Reporter:
                    dcnorris David Norris (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: