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Description
Affects unit tests in TreeLikelihoodWithErrorFastTest, BeagleTreeLikelihoodWithErrorTest, TreeLikelihoodWithErrorSlowTest, and DataTypeTest.
testGT16ErrorLikelihoodCase0() and testGT16ErrorLikelihoodCase1() in TreeLikelihood tests.
Error message for likelihood tests:
Validation error when initializing object beast.base.evolution.alignment.Alignment (id null):
java.lang.IllegalArgumentException: Expected one of [aminoacid, binary, integer, nucleotide, standard, twoStateCovarion, user defined] but got nucleotideDiploid16
at beast.base.core.Input.validate(Unknown Source)
at beast.base.core.BEASTInterface.validateInputs(Unknown Source)
at beast.base.core.BEASTInterface.initByName(Unknown Source)
at phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorFastTest.calculateLikelihoodGT16(TreeLikelihoodWithErrorFastTest.java:302)
at phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorFastTest.testGT16ErrorLikelihoodCase0(TreeLikelihoodWithErrorFastTest.java:440)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
...
java.lang.RuntimeException: validateInputs() failed! Expected one of [aminoacid, binary, integer, nucleotide, standard, twoStateCovarion, user defined] but got nucleotideDiploid16
at beast.base.core.BEASTInterface.initByName(Unknown Source)
at phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorFastTest.calculateLikelihoodGT16(TreeLikelihoodWithErrorFastTest.java:302)
at phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorFastTest.testGT16ErrorLikelihoodCase0(TreeLikelihoodWithErrorFastTest.java:440)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
Error message for DataTypeTest:
java.lang.AssertionError: NucleotideDiploid10
at org.junit.Assert.fail(Assert.java:89)
at org.junit.Assert.assertTrue(Assert.java:42)
at phylonco.beast.evolution.datatype.DataTypeTest.testDataTypes(DataTypeTest.java:57)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
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