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How does GATK find a Walker by name ? ( eclipse plugin)
I'm playing with the GATK jar and I'm trying to use it as an eclipse plugin: that is to say that the GenomeAnalysisTK.jar is itself packaged/bundled in a parent jar. Could this affect the way GATK is finding the walker by name ?
args.toString() is "[-T, CombineVariants, -R, /home/lindenb/src/gatk-ui/testdata/ref.fa, -genotypeMergeOptions, UNIQUIFY, -o, /home/lindenb/jeter.vcf, --variant, /home/lindenb/src/gatk-ui/testdata/S3.vcf.gz, --variant, /home/lindenb/src/gatk-ui/testdata/S4.vcf.gz, --variant, /home/lindenb/src/gatk-ui/testdata/S1.vcf.gz, --variant, /home/lindenb/src/gatk-ui/testdata/S2.vcf.gz]" (...) org.broadinstitute.gatk.utils.exceptions.UserException$MalformedWalkerArgumentsException: Invalid command line: Malformed walker argument: Could not find walker with name: CombineVariants at org.broadinstitute.gatk.engine.WalkerManager.createMalformedArgumentException(WalkerManager.java:165) at org.broadinstitute.gatk.utils.classloader.PluginManager.createByName(PluginManager.java:280) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getWalkerByName(GenomeAnalysisEngine.java:331) at org.broadinstitute.gatk.engine.CommandLineExecutable.getArgumentSources(CommandLineExecutable.java:210) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:205) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) (...)
if yes, is there a way to tell change classLoader ?