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NPE thrown in very rare cases where jannovar fails to fully annotate an intergenic variant #224

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julesjacobsen opened this issue Aug 18, 2017 · 2 comments
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NPE thrown in very rare cases where jannovar fails to fully annotate an intergenic variant #224

julesjacobsen opened this issue Aug 18, 2017 · 2 comments
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@julesjacobsen
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@julesjacobsen
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When an INTERGENIC_VARIANT in a TAD is reassigned to be a REGULATORY_REGION_VARIANT and has not been assigned a gene symbol or identifier by Jannovar a NullPointerException is thrown:

Exception in thread "main" java.lang.NullPointerException
        at org.monarchinitiative.exomiser.core.analysis.util.GeneReassigner.prioritiserScore(GeneReassigner.java:109)
        at org.monarchinitiative.exomiser.core.analysis.util.GeneReassigner.assignVariantToGeneWithHighestPhenotypeScore(GeneReassigner.java:82)
        at org.monarchinitiative.exomiser.core.analysis.util.GeneReassigner.reassignRegulatoryRegionVariantToMostPhenotypicallySimilarGeneInTad(GeneReassigner.java:74)

Fix this so that the variant is either re-assigned to gene in the TAD with the highest prioritiser score, or is left where it is and ignored in the output.
@julesjacobsen julesjacobsen self-assigned this Aug 18, 2017
julesjacobsen added a commit that referenced this issue Aug 21, 2017
@julesjacobsen
Added breaking test to GeneReassignerTest for #224
e393c30
julesjacobsen added a commit that referenced this issue Aug 21, 2017
@julesjacobsen
Fix for #224 and a bit of a tidy-up. Still needs more tidying.
9705fb8
@damiansm
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Tested and looks good to merge back into master and for a hot fix for release 8.0.0

@julesjacobsen
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New release created: https://github.com/exomiser/Exomiser/tree/8.0.1

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