fixed catchall PATH variable bug added trimera to chimera.slayer

[mothur.git] / slayer.cpp

diff --git a/slayer.cpp b/slayer.cpp
index 5d5a48b864695ce2ed92357006b834efa24195bb..72da257848c87485dc674ad5a1e36440e565bbb7 100644 (file)
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -27,7 +27,7 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                                Sequence* q = new Sequence(query->getName(), query->getAligned());
                                Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned());
                                Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned());
-                               
+
                                map<int, int> spots;  //map from spot in original sequence to spot in filtered sequence for query and both parents
                                vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
                                
@@ -37,10 +37,10 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                                        delete rightParent;
                                        return "no"; 
                                }
-                               
+                                       
                                vector<data_struct> selectedDivs;
                                for (int k = 0; k < divs.size(); k++) {
-                               
+                                       
                                        vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
                                        vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
                                        
@@ -105,7 +105,6 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                        }
                }
                
-
                // compute bootstrap support
                if (all.size() > 0) {
                        //sort them
@@ -143,13 +142,13 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
                string parentA = pA->getAligned();
                string parentB = pB->getAligned();
                int length = query.length();
-//cout << q->getName() << endl << q->getAligned() << endl << endl;     
-//cout << pA->getName() << endl << pA->getAligned() << endl << endl;           
-//cout << pB->getName() << endl << pB->getAligned() << endl << endl;   
-//cout << " length = " << length << endl;
-//cout << q->getName() << endl;
-//cout << pA->getName() << '\t';
-//cout << pB->getName() << endl;
+/*cout << q->getName() << endl << q->getAligned() << endl << endl;     
+cout << pA->getName() << endl << pA->getAligned() << endl << endl;             
+cout << pB->getName() << endl << pB->getAligned() << endl << endl;     
+cout << " length = " << length << endl;
+cout << q->getName() << endl;
+cout << pA->getName() << '\t';
+cout << pB->getName() << endl;*/
        
                //check window size
                if (length < (2*windowSize+windowStep)) {