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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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Modelling Somatic Peaks Error #46

Closed DarioS closed 5 years ago

DarioS commented 5 years ago

I tried PURPLE version 2.31 a few minutes ago for the first time and there was an error.

16:47:23 - Modelling somatic peaks
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 201
        at com.hartwig.hmftools.common.variant.clonality.PeakModelFactory.modelPeakHistogram(PeakModelFactory.java:178)
        at com.hartwig.hmftools.common.variant.clonality.PeakModelFactory.model(PeakModelFactory.java:60)
        at com.hartwig.hmftools.purple.PurityPloidyEstimateApplication.modelSomaticPeaks(PurityPloidyEstimateApplication.java:388)
        at com.hartwig.hmftools.purple.PurityPloidyEstimateApplication.<init>(PurityPloidyEstimateApplication.java:192)
        at com.hartwig.hmftools.purple.PurityPloidyEstimateApplication.main(PurityPloidyEstimateApplication.java:96)

I removed -ref_genome and reran the command with version 2.29 and it worked fine. In case it matters, I still have AMBER version 2.1 and COBALT version 1.5 installed because I'm not aware of any version dependencies between the tools. Also, the README file contains a section titled Example Usage but it has not been updated to show the newly mandatory parameter -ref_genome.

jonbaber commented 5 years ago

Thanks Dario.

Vlad just opened a similar ticket so I will close this one. I will release a new version either tonight or tomorrow.

Thanks for letting me know about the example usage. I will fix that as well.

Cheers, Jon