1.19.0

[mothur.git] / slayer.cpp

diff --git a/slayer.cpp b/slayer.cpp
index 877f2414833eb0f54a761fc6f162a4f52e8b5970..4987d4170337f6d4e172c395c137be71832759ed 100644 (file)
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -17,7 +17,7 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
        try {
                vector<data_struct> all; all.clear();
                myQuery = *query;
-               
+
                for (int i = 0; i < refSeqs.size(); i++) {
                
                        for (int j = i+1; j < refSeqs.size(); j++) {
@@ -28,12 +28,17 @@ 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());
+                               
+                               //cout << q->getName() << endl << q->getAligned() << endl << endl;      
+                               //cout << leftParent->getName() << endl << leftParent->getAligned() << endl << endl;            
+                               //cout << rightParent->getName() << endl << rightParent->getAligned() << endl << endl;  
+                               //cout << " length = " << rightParent->getAligned().length() << endl;
        
                                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);
        
                                if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
-                                       
+//                             cout << "examining:\t" << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << endl;
                                vector<data_struct> selectedDivs;
                                for (int k = 0; k < divs.size(); k++) {
                                        
@@ -45,6 +50,7 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                                        int numSNPSLeft = snpsLeft.size();
                                        int numSNPSRight = snpsRight.size();
                                        
+//                                     cout << numSNPSLeft << '\t' << numSNPSRight << endl;
                                        //require at least 4 SNPs on each side of the break
                                        if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
                                                        
@@ -60,16 +66,16 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                                                
                                                
                                                //are we within 10 points of the bootstrap cutoff?
-                                               if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
-                                                       bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
-                                                               
-                                                       if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
-                                                               
-                                                       divs[k].bsa = BS_A;
-                                                       divs[k].bsb = BS_B;
-                                                       divs[k].bsMax = max(BS_A, BS_B);
-                                                       divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
-                                               }
+//                                             if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
+//                                                     bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
+//                                                             
+//                                                     if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
+//                                                             
+//                                                     divs[k].bsa = BS_A;
+//                                                     divs[k].bsb = BS_B;
+//                                                     divs[k].bsMax = max(BS_A, BS_B);
+//                                                     divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
+//                                             }
                                                
                                                //so results reflect orignal alignment
                                                divs[k].winLStart = spots[divs[k].winLStart];
@@ -147,14 +153,14 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
                        int rightLength = length - leftLength;
                                
                        float QLA = computePercentID(query, parentA, 0, breakpoint);
-                       float QRB = computePercentID(query, parentB, breakpoint+1, length);
+                       float QRB = computePercentID(query, parentB, breakpoint+1, length-1);
                
                        float QLB = computePercentID(query, parentB, 0, breakpoint);
-                       float QRA = computePercentID(query, parentA, breakpoint+1, length);
+                       float QRA = computePercentID(query, parentA, breakpoint+1, length-1);
                
                        float LAB = computePercentID(parentA, parentB, 0, breakpoint);
-                       float RAB = computePercentID(parentA, parentB, breakpoint+1, length);
-                                       
+                       float RAB = computePercentID(parentA, parentB, breakpoint+1, length-1); 
+                       
                        float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
                        float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
                        float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
@@ -168,10 +174,11 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
                        float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
                        float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
                        
+                       
                        //cout << q->getName() << '\t';
                        //cout << pA->getName() << '\t';
                        //cout << pB->getName() << '\t';
-                  // cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
+                   //cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
                        //cout << "\tCHIM_TYPE_B\t" << divR_QLB_QRA << "\tQLB: " << QLB << "\tQRA: " << QRA << "\tQLB_QRA: " << QLB_QRA << endl;
 //cout << leftLength << '\t' << rightLength << '\t' << QLA << '\t' << QRB << '\t' << QLB << '\t' << QRA  << '\t' << LAB << '\t' << RAB << '\t' << AB << '\t' << QA << '\t' << QB << '\t' << QLA_QRB << '\t' <<  QLB_QRA <<    endl;                    
 
@@ -216,6 +223,7 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
                        }//if
                }//for
                
+               
                return data;
                
        }