changes for chimera slayer

[mothur.git] / slayer.cpp

diff --git a/slayer.cpp b/slayer.cpp
index 5ecb4ea7c5c430b34efc934b1e736915f363438c..a244ea42634fc9b31218aceaafd3d76f249d92e8 100644 (file)
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -426,21 +426,41 @@ float Slayer::snpAB(vector<snps> data) {
        }
 }
 /***********************************************************************/
-float Slayer::computePercentID(string queryFrag, string parent, int left, int right) {
+float Slayer::computePercentID(string queryAlign, string chimera, int left, int right) {
        try {
-               int total = 0;
-               int matches = 0;
-
+                               
+               int numIdentical = 0;
+               int countA = 0;
+               int countB = 0;
                for (int i = left; i <= right; i++) {
-                       total++;
-                       if (queryFrag[i] == parent[i]) {
-                               matches++;
+                       if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
+                               ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
+                       else {
+                               
+                               bool charA = false; bool charB = false;
+                               if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
+                               if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
+                               
+                               if (charA || charB) {
+                                       
+                                       if (charA) { countA++; }
+                                       if (charB) { countB++; }
+                                       
+                                       if (queryAlign[i] == chimera[i]) {
+                                               numIdentical++;
+                                       }
+                               }
                        }
                }
-
-               float percentID =( matches/(float)total) * 100;
                
-               return percentID;
+               float numBases = (countA + countB) /(float) 2;
+               
+               if (numBases == 0) { return 0; }
+               
+               float percentIdentical = (numIdentical/(float)numBases) * 100;
+               
+               return percentIdentical;
+               
        }
        catch(exception& e) {
                m->errorOut(e, "Slayer", "computePercentID");