fixed jest calc to return only value between 0 and 1. Modified reads …

…in get.seqs, remove.seqs, remove.lineage, get.lineage, screen.seqs, pcr.seqs changed read of count file causing file mismatches with count files that didn't include group data. Fixed bug with make.contigs and reverse index files. Added another file types to fastq.info parse to work towards completion of sra command. Added "NONE" to reverseOligos function.

getlineagecommand.cpp

@@ -492,15 +492,16 @@ int GetLineageCommand::readCount(){
 
         string headers = m->getline(in); m->gobble(in);
         out << headers << endl;
+        string test = headers; vector<string> pieces = m->splitWhiteSpace(test);
 
-        string name, rest; int thisTotal;
+        string name, rest; int thisTotal; rest = "";
         while (!in.eof()) {
 
             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 
             in >> name; m->gobble(in); 
             in >> thisTotal; m->gobble(in);
-            rest = m->getline(in); m->gobble(in);
+            if (pieces.size() > 2) {  rest = m->getline(in); m->gobble(in);  }
             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 
             if (names.count(name) != 0) {

linearalgebra.cpp

@@ -1889,29 +1889,35 @@ void LinearAlgebra::ludcmp(vector<vector<double> >& A, vector<int>& index, doubl
 
 void LinearAlgebra::lubksb(vector<vector<double> >& A, vector<int>& index, vector<double>& b){
     try {
+        //if(m->debug){   m->mothurOut("lubksb\n");    }
         double total;
         int n = (int)A.size();
         int ii = 0;
 
         for(int i=0;i<n;i++){
+            //if(m->debug){   m->mothurOut("i loop " + toString(i) + "\n");    }
             if (m->control_pressed) { break; }
             int ip = index[i];
             total = b[ip];
             b[ip] = b[i];
 
             if (ii != 0) {
                 for(int j=ii-1;j<i;j++){
+                    //if(m->debug){   m->mothurOut("j loop " + toString(j) + "\n");    }
                     total -= A[i][j] * b[j];
                 }
             }
             else if(total != 0){  ii = i+1;   }
             b[i] = total;
         }
         for(int i=n-1;i>=0;i--){
+            //if(m->debug){   m->mothurOut("i loop " + toString(i) + "\n");    }
             total = b[i];
-            for(int j=i+1;j<n;j++){ total -= A[i][j] * b[j];  }
+            for(int j=i+1;j<n;j++){ total -= A[i][j] * b[j];   }
             b[i] = total / A[i][i];
+            //if (A[i][i] == 0) { cout << "ohno!!" << endl; }
         }
+        //if(m->debug){   m->mothurOut("end lubksb\n");    }
     }
 	catch(exception& e) {
 		m->errorOut(e, "LinearAlgebra", "lubksb");
@@ -1922,6 +1928,7 @@ void LinearAlgebra::lubksb(vector<vector<double> >& A, vector<int>& index, vecto
 
 void LinearAlgebra::ludcmp(vector<vector<float> >& A, vector<int>& index, float& d){
     try {
+        //if(m->debug){   m->mothurOut("ludcmp\n");    }
         double tiny = 1e-20;
 
         int n = (int)A.size();
@@ -1932,6 +1939,7 @@ void LinearAlgebra::ludcmp(vector<vector<float> >& A, vector<int>& index, float&
         d = 1.0;
 
         for(int i=0;i<n;i++){
+            //if(m->debug){   m->mothurOut("i loop " + toString(i) + "\n");    }
             float big = 0.0;
             for(int j=0;j<n;j++){   if((temp=fabs(A[i][j])) > big ) big=temp;  }
             if(big==0.0){   m->mothurOut("Singular matrix in routine ludcmp\n");    }
@@ -1940,14 +1948,17 @@ void LinearAlgebra::ludcmp(vector<vector<float> >& A, vector<int>& index, float&
 
         for(int j=0;j<n;j++){
             if (m->control_pressed) { break; }
+            //if(m->debug){   m->mothurOut("j loop " + toString(j) + "\n");    }
             for(int i=0;i<j;i++){
+                //if(m->debug){   m->mothurOut("i loop " + toString(i) + "\n");    }
                 float sum = A[i][j];
                 for(int k=0;k<i;k++){   sum -= A[i][k] * A[k][j];   }
                 A[i][j] = sum;
             }
 
             float big = 0.0;
             for(int i=j;i<n;i++){
+                //if(m->debug){   m->mothurOut("j loop " + toString(j) + "\n");    }
                 float sum = A[i][j];
                 for(int k=0;k<j;k++){   sum -= A[i][k] * A[k][j];   }
                 A[i][j] = sum;
@@ -1975,6 +1986,7 @@ void LinearAlgebra::ludcmp(vector<vector<float> >& A, vector<int>& index, float&
                 for(int i=j+1;i<n;i++){ A[i][j] *= dum; }
             }
         }
+        //if(m->debug){   m->mothurOut("end ludcmp\n");    }
     }
 	catch(exception& e) {
 		m->errorOut(e, "LinearAlgebra", "ludcmp");

makecontigscommand.cpp

@@ -977,7 +977,7 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
 
             if (thisrindexfile != "") {
                 Sequence temp(inRIndex); m->gobble(inRIndex);
-                rindexBarcode.setAligned(temp.getAligned());
+                rindexBarcode.setAligned(trimOligos.reverseOligo(temp.getAligned()));
             }
 
             int barcodeIndex = 0;

oligos.cpp

@@ -461,6 +461,9 @@ map<int, oligosPair> Oligos::getReorientedPairedBarcodes(){
 //********************************************************************/
 string Oligos::reverseOligo(string oligo){
 	try {
+
+        if (oligo == "NONE") { return "NONE"; }
+
         string reverse = "";
 
         for(int i=oligo.length()-1;i>=0;i--){