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PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool
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2.8.1 DPYD: java.lang.ArrayIndexOutOfBoundsException: Index 2 out of bounds for length 2 #156

Closed hudja closed 11 months ago

hudja commented 11 months ago

Hi,

sorry, but I have bad news concerning DPYD again... I am using 2.8.1 PharmCat and 2.8.1 preprocessor.

java -jar pharmcat-2.8.1-all.jar -vcf test.vcf.gz -o ./
java.lang.ArrayIndexOutOfBoundsException: Index 2 out of bounds for length 2
    at org.pharmgkb.pharmcat.haplotype.model.CombinationMatch.buildHaplotype(CombinationMatch.java:129)
    at org.pharmgkb.pharmcat.haplotype.model.CombinationMatch.merge(CombinationMatch.java:177)
    at org.pharmgkb.pharmcat.haplotype.DpydHapB3Matcher.updateHapB3Haplotype(DpydHapB3Matcher.java:252)
    at org.pharmgkb.pharmcat.haplotype.DpydHapB3Matcher.buildDiplotype(DpydHapB3Matcher.java:205)
    at org.pharmgkb.pharmcat.haplotype.DpydHapB3Matcher.mergePhasedDiplotypeMatch(DpydHapB3Matcher.java:198)
    at org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher.callDpyd(NamedAlleleMatcher.java:310)
    at org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher.call(NamedAlleleMatcher.java:202)
    at org.pharmgkb.pharmcat.Pipeline.call(Pipeline.java:233)
    at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:166)

VCF body which produces an error. Phased data. Other sites are REFs.

chr1    97305364    .   C   T   .   .   .   GT  1|0
chr1    97515839    .   T   C   .   .   .   GT  1|0
chr1    97573863    .   C   T   .   .   .   GT  1|0
chr1    97579893    .   G   C   .   .   .   GT  1|0

Test VCF file. https://www.dropbox.com/scl/fi/5cso1hdhz3fhypnlw9jp0/test.vcf.gz?rlkey=m4ik7mjx0897xi3q5prqbrkaq&dl=0

Thank you!

markwoon commented 11 months ago

I've got a fix for this. That included VCF simplifies things. BTW, you can also just drag and drop files into GitHub to attach it to an issue (you may have to zip it up first).

Could you please try this out and see if you run into any more problems: pharmcat-2.8.1-1-ga29420a4-all.zip

Unzip and use this instead of your existing pharmcat-xxx-all.jar.

If you don't find any more problems, I'll cut a new release.

Thanks.

hudja commented 11 months ago

Hi, it seems working fine now! Thank you for the quick response!