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Custom Walker :

lindenblindenb FranceMember ✭✭

Hi all,

I'm playing with the GATK3.6 API, writing a custom walker.

@DocumentedGATKFeature(
        summary="Annotate Variants with eigen data",
        groupName = HelpConstants.DOCS_CAT_VARMANIP,
        extraDocs = {CommandLineGATK.class}
        )
public class EigenVariants extends AbstractVariantProcessor {
public abstract class AbstractVariantProcessor
extends RodWalker<Long, Long> implements TreeReducible<Long>
{
    @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
    protected RodBinding<VariantContext> variants;

    @Output(doc="File to which variants should be written")
    protected VariantContextWriter writer = null;
(...)

I'm compiling, packaging & everything is fine:

$  java -cp GenomeAnalysisTK.jar:mygatk.jar org.broadinstitute.gatk.engine.CommandLineGATK -T EigenVariants --help
(...)
Arguments for EigenVariants:
 -eigen,--eigenDirectory <eigenDirectory>   The Eigen directory
 -V,--variant <variant>                     Input VCF file
 -o,--out <out>                             File to which variants should be written
(...)

but when I only add one import from my source (no variable, only the import):

import com.github.lindenb.jvarkit.tools.vcfeigen.EigenInfoAnnotator;

then the PluginManager goes mad:

$  java -cp GenomeAnalysisTK.jar:mygatk.jar org.broadinstitute.gatk.engine.CommandLineGATK -T EigenVariants --help
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.6-0-g89b7209): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Could not create module CodingFeatureCodec because Cannot instantiate class (Illegal Access) caused by exception Class org.broadinstitute.gatk.utils.classloader.PluginManager can not access a member of class com.github.lindenb.jvarkit.tools.vcfeigen.EigenInfoAnnotator$CodingFeatureCodec with modifiers "private"
##### ERROR ------------------------------------------------------------------------------------------

why ? how can i fix this ? thanks !

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