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Need to change bounds for slice sampling of variance in copy-ratio model. #804

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samuelklee opened this issue Nov 29, 2016 · 0 comments · Fixed by #1001
Closed

Need to change bounds for slice sampling of variance in copy-ratio model. #804

samuelklee opened this issue Nov 29, 2016 · 0 comments · Fixed by #1001
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@samuelklee samuelklee commented Nov 29, 2016

Got a weird sample (possibly with high variance?) that threw an exception. Should be a simple fix to change the hard-coded min/max variance to instead use values derived from the data:

java.lang.IllegalArgumentException: Initial point in slice sampler is not within specified range.
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:609)
at org.broadinstitute.hellbender.utils.mcmc.SliceSampler.sample(SliceSampler.java:71)
at org.broadinstitute.hellbender.tools.exome.copyratio.CopyRatioSamplers$VarianceSampler.sample(CopyRatioSamplers.java:54)
at org.broadinstitute.hellbender.tools.exome.copyratio.CopyRatioSamplers$VarianceSampler.sample(CopyRatioSamplers.java:29)
at org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.doGibbsUpdate(ParameterizedModel.java:134)
at org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.update(ParameterizedModel.java:124)
at org.broadinstitute.hellbender.utils.mcmc.GibbsSampler.runMCMC(GibbsSampler.java:76)
at org.broadinstitute.hellbender.tools.exome.copyratio.CopyRatioModeller.fitMCMC(CopyRatioModeller.java:96)
at org.broadinstitute.hellbender.tools.exome.ACNVModeller.fitModel(ACNVModeller.java:145)
at org.broadinstitute.hellbender.tools.exome.ACNVModeller.performSimilarSegmentMergingIteration(ACNVModeller.java:126)
at org.broadinstitute.hellbender.tools.exome.AllelicCNV.performSimilarSegmentMergingStep(AllelicCNV.java:391)
at org.broadinstitute.hellbender.tools.exome.AllelicCNV.runPipeline(AllelicCNV.java:288)
at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:108)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:166)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:76)
at org.broadinstitute.hellbender.Main.main(Main.java:92)
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