Merge pull request #37 from ComparativeGenomicsToolkit/chop

fix bug in removeDupes
ComparativeGenomicsToolkit · Feb 10, 2021 · 91a7569 · 91a7569
2 parents cff3d34 + 06073dd
commit 91a7569
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/halRemoveDupes.cpp b/halRemoveDupes.cpp
@@ -65,8 +65,11 @@ int main(int argc, char** argv) {
             TopSegment* topSeg = topIt->tseg();
             if (topSeg->hasNextParalogy()) {
                 topSeg->setNextParalogyIndex(NULL_INDEX);
-                total_length += topSeg->getLength();
-                ++total_edges;
+                if (!topSeg->isCanonicalParalog()) {
+                    topSeg->setParentIndex(NULL_INDEX);
+                    total_length += topSeg->getLength();
+                    ++total_edges;
+                }
             }
         }