[med-svn] [iqtree] 02/03: Imported Upstream version 1.3.14+dfsg

[Andreas Tille]

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tille pushed a commit to branch master
in repository iqtree.

commit 79edd159e7488de9093ae70c64a57f3cd211fb2e
Author: Andreas Tille <tille at debian.org>
Date:   Sun Feb 7 21:59:04 2016 +0100

    Imported Upstream version 1.3.14+dfsg
---
 CMakeLists.txt        | 2 +-
 alignmentpairwise.cpp | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 61cad8a..04b998b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -45,7 +45,7 @@ add_definitions(-DIQ_TREE)
 # The version number.
 set (iqtree_VERSION_MAJOR 1)
 set (iqtree_VERSION_MINOR 3)
-set (iqtree_VERSION_PATCH "13") 
+set (iqtree_VERSION_PATCH "14") 
 
 set(BUILD_SHARED_LIBS OFF)
 
diff --git a/alignmentpairwise.cpp b/alignmentpairwise.cpp
index 38b30a2..92f21cd 100644
--- a/alignmentpairwise.cpp
+++ b/alignmentpairwise.cpp
@@ -270,7 +270,8 @@ void AlignmentPairwise::computeFuncDerv(double value, double &df, double &ddf) {
             sum_derv2[i] += trans_derv2[i] * rate_sqr;
         }
     }
-    for (i = 0; i < trans_size; i++) if (pair_freq[i] > Params::getInstance().min_branch_length) {
+    for (i = 0; i < trans_size; i++) 
+        if (pair_freq[i] > Params::getInstance().min_branch_length && sum_trans[i] > 0) {
 //            lh -= pair_freq[i] * log(sum_trans[i]);
             double d1 = sum_derv1[i] / sum_trans[i];
             df -= pair_freq[i] * d1;

-- 
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