tracking down chimera.slayer issue

[mothur.git] / slayer.cpp

diff --git a/slayer.cpp b/slayer.cpp
index 72da257848c87485dc674ad5a1e36440e565bbb7..ba1bf337d4084e58416b06c48cb6a359bb5b05b1 100644 (file)
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -38,6 +38,7 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                                        return "no"; 
                                }
                                        
+//                             cout << divs.size() << endl;
                                vector<data_struct> selectedDivs;
                                for (int k = 0; k < divs.size(); k++) {
                                        
@@ -55,7 +56,8 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                                        int numSNPSRight = snpsRight.size();
                                        
                                        //require at least 3 SNPs on each side of the break
-                                       if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) {
+//                                     if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) {
+                                       if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
                                        
                                                //removed in 12/09 version of chimeraSlayer
                                                //int winSizeLeft = divs[k].winLEnd - divs[k].winLStart + 1;
@@ -152,7 +154,7 @@ cout << pB->getName() << endl;*/
        
                //check window size
                if (length < (2*windowSize+windowStep)) { 
-                       m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine();        
+//                     m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine();        
                        windowSize = length / 4;
                }
                
@@ -275,6 +277,7 @@ vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int l
                                        data.push_back(member);
                                }
                        }
+//                     cout << i << '\t' << data.size() << endl;
                }
                
                return data;