Details
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Type: Task
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Status: Closed (View Workflow)
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Priority: Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.0.2 Minor Release
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Labels:
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Story Points:2
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Sprint:Fall 2018 Sprint 3, Fall 2018 Sprint 4
Description
IGV codebase has updated bigbed and bigwig parsing code.
We are currently using very old versions of this same code, packaged in artifact bigwig-1.0.jar.
This older artifact bigwig-1.0.jar uses SeekableStream and SeakableStreamReader classes from another very old artifact - tribble-0.1.jar, which is packaged into the bigwig-1.0.jar artifact.
However, elsewhere in the project we are now using an htsjdk artifact which contains SeekableStream and SeakableStreamReader classes that can replace same in tribble-0.1.jar. In addition, newer igv code is using these same classes.
To simplify the code base - and make the final packaged jar files smaller - we will build a new bundle containing IGV bigbed and bigwig parsing code that uses the htsjdk artifact, which will be provided as a bundle by the OSGi framework.
This new bundle should be as lightweight as possible - it should include just packages we need and include logging code used by the rest of the IGB code base.
To build the bundle, we will 1st fork the igv code base and add new scripts (or gradle/maven build configuration files) to build the bundle we want. We will also modify the igv code base as required to use our preferred logging framework. We will do this in such a way as to enable us to keep our fork up-to-date with the IGV code base.
Packages required:
org.broad.igv.bbfile
Package may be required - check in IGB code base to be sure:
org.broad.igv.bigwig