]> git.donarmstrong.com Git - mothur.git/blobdiff - slayer.cpp
added modify names parameter to set.dir
[mothur.git] / slayer.cpp
index 8e9eb56c8e55bddd9405cc790759c45f2ed7dc12..a787f2727dd8290b89bffeb382bae6c15001110d 100644 (file)
 #include "slayer.h"
 
 /***********************************************************************/
-Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i) :
-               windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i){}
+Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp, int mi) :
+               minBS(mi), windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
 /***********************************************************************/
-string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
+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++) {
                        
+                               if (m->control_pressed) { return "no";  }
+       
                                //make copies of query and each parent because runBellerophon removes gaps and messes them up
-                               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());
-                               
-                               vector<data_struct> divs = runBellerophon(q, leftParent, rightParent);
+                               Sequence q(query.getName(), query.getAligned());
+                               Sequence leftParent(refSeqs[i].getName(), refSeqs[i].getAligned());
+                               Sequence rightParent(refSeqs[j].getName(), refSeqs[j].getAligned());
                                
+                               //cout << q->getName() << endl << q->getAligned() << endl << endl;      
+                               //cout << leftParent.getName() << '\t' << leftParent.getAligned().length() << endl << endl;
+                               //cout << rightParent.getName() << '\t' << rightParent.getAligned().length() << endl << endl;
+                               //cout << q.getName() << '\t' << q.getAligned().length() << 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) { 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++) {
-                               
+                                       
                                        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);
+       
+                                       if (m->control_pressed) {  return "no"; }
                                        
                                        int numSNPSLeft = snpsLeft.size();
                                        int numSNPSRight = snpsRight.size();
                                        
-                                       //require at least 3 SNPs on each side of the break
-                                       if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) {
-                                               
-                                               int winSizeLeft = divs[k].winLEnd - divs[k].winLStart + 1;
-                                               int winSizeRight = divs[k].winREnd - divs[k].winRStart + 1;
-                                               
-                                               float snpRateLeft = numSNPSLeft / (float) winSizeLeft;
-                                               float snpRateRight = numSNPSRight / (float) winSizeRight;
-                                               float logR = log(snpRateLeft / snpRateRight) / log(2.0);
-                                               
-                                               // do not accept excess snp ratio on either side of the break
-                                               if (abs(logR) < 1 ) {  
+//                                     cout << numSNPSLeft << '\t' << numSNPSRight << endl;
+                                       //require at least 4 SNPs on each side of the break
+                                       if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
                                                        
-                                                       float BS_A, BS_B;
-                                                       bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B);
+                                               float BS_A, BS_B;
+                                               bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters);
+                                               
+                                               if (m->control_pressed) { return "no"; }
 
-                                                       divs[k].bsa = BS_A;
-                                                       divs[k].bsb = BS_B;
+                                               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);
+                                               
                                                
-                                                       divs[k].bsMax = max(BS_A, BS_B);
+                                               //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);
+//                                             }
                                                
-                                                       divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
+                                               //so results reflect orignal alignment
+                                               divs[k].winLStart = spots[divs[k].winLStart];
+                                               divs[k].winLEnd = spots[divs[k].winLEnd];  
+                                               divs[k].winRStart = spots[divs[k].winRStart]; 
+                                               divs[k].winREnd = spots[divs[k].winREnd]; 
                                                
-                                                       selectedDivs.push_back(divs[k]);
-                                               }
+                                               selectedDivs.push_back(divs[k]);
                                        }
                                }
-                               
+
                                //save selected
-                               for (int m = 0; m < selectedDivs.size(); m++) {  all.push_back(selectedDivs[m]);        }
-                               
-                               delete q;
-                               delete leftParent;
-                               delete rightParent;
+                               for (int mi = 0; mi < selectedDivs.size(); mi++) {  all.push_back(selectedDivs[mi]);    }
                        }
                }
                
-               
+
                // compute bootstrap support
                if (all.size() > 0) {
                        //sort them
                        sort(all.begin(), all.end(), compareDataStruct);
                        reverse(all.begin(), all.end());
-                       
+                                               
                        outputResults = all;
                        return "yes"; 
-               }
-               else {
+               }else {
                        outputResults = all;
                        return "no";
                }
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "getResults");
+               m->errorOut(e, "Slayer", "getResults");
                exit(1);
        }
 }
 /***********************************************************************/
-vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB) {
+vector<data_struct> Slayer::runBellerophon(Sequence q, Sequence pA, Sequence pB, map<int, int>& spots) {
        try{
                
                vector<data_struct> data;
-                               
+               
                //vertical filter
-               vector<Sequence*> temp;
-               temp.push_back(q); temp.push_back(pA); temp.push_back(pB);
-               map<int, int> spots = verticalFilter(temp);
+               //cout << q.getName() << endl << q.getAligned() << endl << endl;        
+               //cout << pA.getName() << endl << pA.getUnaligned() << endl << endl;            
+               //cout << pB.getName() << endl << pB.getUnaligned() << endl << endl;    
+               
+               //maps spot in new alignment to spot in alignment before filter
+               spots = verticalFilter(q, pA, pB);  //fills baseSpots
                
                //get these to avoid numerous function calls
-               string query = q->getAligned();
-               string parentA = pA->getAligned();
-               string parentB = pB->getAligned();
+               string query = q.getAligned();
+               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.getUnaligned() << endl << endl;           
+//cout << pB.getName() << endl << pB.getUnaligned() << endl << endl;   
+//cout << " length = " << length << endl;
+       
                //check window size
                if (length < (2*windowSize+windowStep)) { 
-                       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."); 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;
                }
                
                for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
                
+                       if (m->control_pressed) { return data; }
+               
                        int breakpoint = i;
                        int leftLength = breakpoint + 1;
                        int rightLength = length - leftLength;
-                       
+                               
                        float QLA = computePercentID(query, parentA, 0, breakpoint);
-                       float QRB = computePercentID(query, parentB, breakpoint+1, length - 1);
+                       float QRB = computePercentID(query, parentB, breakpoint+1, length-1);
                
                        float QLB = computePercentID(query, parentB, 0, breakpoint);
-                       float QRA = computePercentID(query, parentA, breakpoint+1, length - 1);
+                       float QRA = computePercentID(query, parentA, breakpoint+1, length-1);
                
                        float LAB = computePercentID(parentA, parentB, 0, breakpoint);
-                       float RAB = computePercentID(parentA, parentB, breakpoint+1, length - 1);
-               
+                       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;
@@ -143,9 +171,18 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
                        //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length;
                
                        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 << "\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;                    
 
+//cout << divRThreshold << endl;
+//cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl;
                        //is one of them above the 
                        if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) {
                                
@@ -167,13 +204,13 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
                                        member.rab = RAB; 
                                        member.qra = QRA; 
                                        member.qlb = QLB; 
-                                       member.winLStart = spots[0];
-                                       member.winLEnd = spots[breakpoint];  //so breakpoint reflects spot in alignment before filter
-                                       member.winRStart = spots[breakpoint+1]
-                                       member.winREnd = spots[length-1]
-                                       member.querySeq = *(q); 
-                                       member.parentA = *(pA);
-                                       member.parentB = *(pB);
+                                       member.winLStart = 0;
+                                       member.winLEnd = breakpoint;  
+                                       member.winRStart = breakpoint+1
+                                       member.winREnd = length-1
+                                       member.querySeq = q;
+                                       member.parentA = pA;
+                                       member.parentB = pB;
                                        member.bsa = 0;
                                        member.bsb = 0;
                                        member.bsMax = 0;
@@ -185,11 +222,12 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
                        }//if
                }//for
                
+               
                return data;
                
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "runBellerophon");
+               m->errorOut(e, "Slayer", "runBellerophon");
                exit(1);
        }
 }
@@ -206,12 +244,30 @@ vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int l
                        char B = parentB[i];
                        
                        if ((A != Q) || (B != Q)) {
-                               snps member;
-                               member.queryChar = Q;
-                               member.parentAChar = A;
-                               member.parentBChar = B;
+
+                               //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS
+
                                
-                               data.push_back(member);
+                               if (
+                                       //did query loose a base here during filter??
+                                       ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) &&
+                                       ( i == query.length()-1 || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
+                                       &&
+                                       //did parentA loose a base here during filter??
+                                       ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) &&
+                                       ( i == parentA.length()-1 || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1) 
+                                       &&
+                                       //did parentB loose a base here during filter??
+                                       ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) &&
+                                       ( i == parentB.length()-1 || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
+                                       ) 
+                               { 
+                                       snps member;
+                                       member.queryChar = Q;
+                                       member.parentAChar = A;
+                                       member.parentBChar = B;
+                                       data.push_back(member);
+                               }
                        }
                }
                
@@ -219,12 +275,12 @@ vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int l
                
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "getSNPS");
+               m->errorOut(e, "Slayer", "getSNPS");
                exit(1);
        }
 }
 /***********************************************************************/
-void Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB) {
+int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB, int numIters) {
        try {
 
                srand((unsigned)time( NULL ));
@@ -232,12 +288,14 @@ void Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, fl
                int count_A = 0; // sceneario QLA,QRB supported
                int count_B = 0; // sceneario QLB,QRA supported
        
-               int numLeft = max(1, int(left.size()/10 +0.5));
-               int numRight = max(1, int(right.size()/10 + 0.5));
-               
-               for (int i = 0; i < iters; i++) {
+               int numLeft = max(1, int(left.size() * percentSNPSample/(float)100 + 0.5));
+               int numRight = max(1, int(right.size() * percentSNPSample/(float)100 + 0.5));
+
+               for (int i = 0; i < numIters; i++) {
                        //random sampling with replacement.
                
+                       if (m->control_pressed) { return 0;  }
+                       
                        vector<snps> selectedLeft;
 
                        for (int j = 0; j < numLeft; j++) {
@@ -278,15 +336,35 @@ void Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, fl
                        if ((QLB > QLA) && (QRA > QRB)) {
                                count_B++;
                        }
-               
+                       
+//cout << "selected left snp: \n";
+//for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentAChar;  } 
+//cout << endl;
+//for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].queryChar;  }
+//cout << endl;
+//for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentBChar;  }
+//cout << endl;
+//cout << "selected right snp: \n";
+//for (int j = 0; j < selectedRight.size(); j++) {  cout << selectedRight[j].parentAChar;  } 
+//cout << endl;
+//for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].queryChar;  }
+//cout << endl;
+//for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].parentBChar;  }
+//cout << endl;                
                }
 
-               BSA = ((float) count_A / (float) iters) * 100;
-               BSB = ((float) count_B / (float) iters) * 100;
+
+               //cout << count_A << '\t' << count_B << endl;
+
+               BSA = (float) count_A / (float) numIters * 100;
+               BSB = (float) count_B / (float) numIters * 100;
+//cout << "bsa = " << BSA << " bsb = " << BSB << endl;
+
+               return 0;
        
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "bootstrapSNPS");
+               m->errorOut(e, "Slayer", "bootstrapSNPS");
                exit(1);
        }
 }
@@ -307,7 +385,7 @@ float Slayer::snpQA(vector<snps> data) {
                return percentID;
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "snpQA");
+               m->errorOut(e, "Slayer", "snpQA");
                exit(1);
        }
 }
@@ -329,7 +407,7 @@ float Slayer::snpQB(vector<snps> data) {
 
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "snpQB");
+               m->errorOut(e, "Slayer", "snpQB");
                exit(1);
        }
 }
@@ -350,82 +428,159 @@ float Slayer::snpAB(vector<snps> data) {
 
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "snpAB");
+               m->errorOut(e, "Slayer", "snpAB");
                exit(1);
        }
 }
 /***********************************************************************/
-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 numBases = (countA + countB) /(float) 2;
+               
+               if (numBases == 0) { return 0; }
+               
+               float percentIdentical = (numIdentical/(float)numBases) * 100;
 
-               float percentID =( matches/(float)total) * 100;
+               return percentIdentical;
                
-               return percentID;
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "computePercentID");
+               m->errorOut(e, "Slayer", "computePercentID");
                exit(1);
        }
 }
 /***********************************************************************/
 //remove columns that contain any gaps
-map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
+map<int, int> Slayer::verticalFilter(Sequence& q, Sequence& pA, Sequence& pB) {
        try {
-               vector<int> gaps;       gaps.resize(seqs[0]->getAligned().length(), 0);
+               //find baseSpots
+               baseSpots.clear(); 
+               baseSpots.resize(3);  //query, parentA, parentB
+       
+               vector<int> gaps;       gaps.resize(q.getAligned().length(), 0);
                
-               string filterString = (string(seqs[0]->getAligned().length(), '1'));
+               string filterString = (string(q.getAligned().length(), '1'));
                
-               //for each sequence
-               for (int i = 0; i < seqs.size(); i++) {
+               string seqAligned = q.getAligned();
+               for (int j = 0; j < seqAligned.length(); j++) {
+                       //if this spot is a gap
+                       if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
+               }
                
-                       string seqAligned = seqs[i]->getAligned();
-                       
-                       for (int j = 0; j < seqAligned.length(); j++) {
-                               //if this spot is a gap
-                               if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {       gaps[j]++;      }
-                       }
+               seqAligned = pA.getAligned();
+               for (int j = 0; j < seqAligned.length(); j++) {
+                       //if this spot is a gap
+                       if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
+               }
+               
+               seqAligned = pB.getAligned();
+               for (int j = 0; j < seqAligned.length(); j++) {
+                       //if this spot is a gap
+                       if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
                }
                
-               //zero out spot where all sequences have blanks
+               
+               //zero out spot where any sequences have blanks
                int numColRemoved = 0;
                int count = 0;
                map<int, int> maskMap; maskMap.clear();
 
-               for(int i = 0; i < seqs[0]->getAligned().length(); i++){
+               for(int i = 0; i < q.getAligned().length(); i++){
                        if(gaps[i] != 0)        {       filterString[i] = '0';  numColRemoved++;  }
                        else {
                                maskMap[count] = i;
                                count++;
                        }
                }
+
+               seqAligned = q.getAligned();
+               string newAligned = "";
+                       
+               int baseCount = 0;
+               count = 0;
+               for (int j = 0; j < seqAligned.length(); j++) {
+                       //are you a base
+                       if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
+                       
+                       //if this spot is not a gap
+                       if (filterString[j] == '1') { 
+                               newAligned += seqAligned[j]; 
+                               baseSpots[0][count] = baseCount;
+                               count++;
+                       }
+               }
+                       
+               q.setAligned(newAligned);
                
-               //for each sequence
-               for (int i = 0; i < seqs.size(); i++) {
+               seqAligned = pA.getAligned();
+               newAligned = "";
                
-                       string seqAligned = seqs[i]->getAligned();
-                       string newAligned = "";
+               baseCount = 0;
+               count = 0;
+               for (int j = 0; j < seqAligned.length(); j++) {
+                       //are you a base
+                       if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
                        
-                       for (int j = 0; j < seqAligned.length(); j++) {
-                               //if this spot is not a gap
-                               if (filterString[j] == '1') { newAligned += seqAligned[j]; }
+                       //if this spot is not a gap
+                       if (filterString[j] == '1') { 
+                               newAligned += seqAligned[j]; 
+                               baseSpots[1][count] = baseCount;
+                               count++;
                        }
+               }
+               
+               pA.setAligned(newAligned);
+               
+               seqAligned = pB.getAligned();
+               newAligned = "";
+               
+               baseCount = 0;
+               count = 0;
+               for (int j = 0; j < seqAligned.length(); j++) {
+                       //are you a base
+                       if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
                        
-                       seqs[i]->setAligned(newAligned);
+                       //if this spot is not a gap
+                       if (filterString[j] == '1') { 
+                               newAligned += seqAligned[j]; 
+                               baseSpots[2][count] = baseCount;
+                               count++;
+                       }
                }
                
+               pB.setAligned(newAligned);
+               
+               
                return maskMap;
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "verticalFilter");
+               m->errorOut(e, "Slayer", "verticalFilter");
                exit(1);
        }
 }