From e6fd7524f063079b42cf3e8b9ff0a6d1bdb79700 Mon Sep 17 00:00:00 2001
From: jordandouglas <jordandouglas@windowslive.com>
Date: Mon, 23 Sep 2024 13:02:07 +1200
Subject: [PATCH] fix indexing error in beagle tree likellihood fixes #1168

---
 src/beast/base/evolution/likelihood/BeagleTreeLikelihood.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/beast/base/evolution/likelihood/BeagleTreeLikelihood.java b/src/beast/base/evolution/likelihood/BeagleTreeLikelihood.java
index f6f36889..679f94d2 100644
--- a/src/beast/base/evolution/likelihood/BeagleTreeLikelihood.java
+++ b/src/beast/base/evolution/likelihood/BeagleTreeLikelihood.java
@@ -959,7 +959,7 @@ private int traverse(Node node, int[] operatorNumber, boolean flip) {
             matrixUpdateIndices[eigenIndex][updateCount] = matrixBufferHelper.getOffsetIndex(nodeNum);
 
             if (substitutionModel.canReturnComplexDiagonalization()) {
-                for (int i = 0; i < m_siteModel.getCategoryCount(); i++) {
+                for (int i = 0; i < this.categoryCount; i++) {
                     final double jointBranchRate = m_siteModel.getRateForCategory(i, node) * branchRate;
                     substitutionModel.getTransitionProbabilities(node, node.getParent().getHeight(), node.getHeight(), jointBranchRate, probabilities);
                     //System.out.println(node.getNr() + " " + Arrays.toString(m_fProbabilities));