qcoverage uses JAXB for the serialisation of java objects into an xml report. The jar files that the JAXB implementation depends on are housed within java's rt.jar in versions of java up to version 8. Version 9 and 10 contain the relevant jar files, but they have been deprecated, and from version 11 onwards, they have been removed.
If you run the current released qcoverage code (/software/adamajava/adamajava-release/123.cdccef6/) using java 11, a ClassNotFoundException is thrown.
Unfortunately, the simple fix of adding the JAXB dependancies didn't work, due to ClassLoader issues, and so the simplest way I could find to fix this was to use the JAXB implementation from eclipse, called MOXy.
The build file was amended to bring in the jakarta JAXB bindings jar, along with the MOXy jar.
The model classes (QCoverageSpec, CoverageModel and CoverageReport) were refactored to import from the different dependencies and tests were added.
Type of change
Refactoring to ready the codebase for newer java versions
How Has This Been Tested?
Additional tests have been added and the updated code has been run against a bam and the results favourably compared with the previous versions reults.
Are WDL Updates Required?
n/a
Checklist:
[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[X] My changes generate no new warnings
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes
Description
qcoverageusesJAXBfor the serialisation of java objects into an xml report. The jar files that theJAXBimplementation depends on are housed within java'srt.jarin versions of java up to version 8. Version 9 and 10 contain the relevant jar files, but they have been deprecated, and from version 11 onwards, they have been removed.More info here.
If you run the current released
qcoveragecode (/software/adamajava/adamajava-release/123.cdccef6/) using java 11, aClassNotFoundExceptionis thrown.Unfortunately, the simple fix of adding the
JAXBdependancies didn't work, due to ClassLoader issues, and so the simplest way I could find to fix this was to use theJAXBimplementation fromeclipse, called MOXy.The build file was amended to bring in the
jakartaJAXB bindings jar, along with theMOXyjar. The model classes (QCoverageSpec,CoverageModelandCoverageReport) were refactored to import from the different dependencies and tests were added.Type of change
Refactoring to ready the codebase for newer java versions
How Has This Been Tested?
Additional tests have been added and the updated code has been run against a bam and the results favourably compared with the previous versions reults.
Are WDL Updates Required?
n/a
Checklist: