Fix 4dExtract problem w/ intra-exon duplication

(hopefully)
ComparativeGenomicsToolkit · Nov 15, 2013 · bba26fe · bba26fe
1 parent 01df73c
commit bba26fe
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/extract/impl/hal4dExtract.cpp b/extract/impl/hal4dExtract.cpp
@@ -264,9 +264,11 @@ void Extract4d::extractConservedBlocks4d()
           if (reversed) {
             colIt->toSite(colIt->getReferenceSequencePosition() + _refSequence->getStartPosition() - 1,
                           colIt->getReferenceSequencePosition() + _refSequence->getStartPosition(),
-                          false);
+                          true);
           } else {
-            colIt->toRight();
+            colIt->toSite(colIt->getReferenceSequencePosition() + _refSequence->getStartPosition() + 1,
+                          colIt->getReferenceSequencePosition() + _refSequence->getStartPosition() + 2,
+                          true);
           }
         }
       }