small mod to chimerarefseq.cpp

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index 4d4a658fe471ba9d0970fbb7fa57151d93c53807..aab17e6b50d1c966f53c7d56e05c383507237a27 100644 (file)
--- a/refchimeratest.cpp
+++ b/refchimeratest.cpp
@@ -60,12 +60,8 @@ int RefChimeraTest::analyzeQuery(string queryName, string querySeq){
        int nMera = 0;
        string chimeraRefSeq = "";
        
-       if(bestSequenceMismatch - minMismatchToChimera <= 3){
-               nMera = 1;
-               chimeraRefSeq = referenceSeqs[bestMatch];
-       }
-       else {
-
+       if(bestSequenceMismatch - minMismatchToChimera > 3 || (minMismatchToChimera == 0 && bestSequenceMismatch != 0)){
+       
                nMera = 2;
                chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
                
@@ -81,6 +77,12 @@ int RefChimeraTest::analyzeQuery(string queryName, string querySeq){
 //             }
                
        }
+       else{
+               nMera = 1;
+               chimeraRefSeq = referenceSeqs[bestMatch];
+       }
+       
+       
        double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
        
 //     double loonIndex = calcLoonIndex(querySeq, referenceSeqs[leftParentBi], referenceSeqs[rightParentBi], breakPointBi, binMatrix);