working on pam

[mothur.git] / makecontigscommand.cpp

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index 0bf56e7c2166daf33816de12216d318a5fba466b..8796ab2113f455b12c8eace90df64d4bbe2c318e 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -1042,7 +1042,9 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
             
             int oStart = contig.length();
+            //cout << fSeq.getAligned()  << endl; cout << rSeq.getAligned() << endl;
             for (int i = overlapStart; i < overlapEnd; i++) {
+                //cout << seq1[i] << ' ' << seq2[i] << ' ' << scores1[ABaseMap[i]] << ' ' << scores2[BBaseMap[i]] << endl;
                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
                     contig += seq1[i];
                 }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below insert. In that case eliminate base
@@ -1076,7 +1078,8 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
             }else { //seq2 ends before seq1 so take from overlap to length from seq1
                 for (int i = overlapEnd; i < length; i++) {  contig += seq1[i]; }
             }
-            
+            //cout << contig << endl;
+            //exit(1);
             if (trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart);  if (contig.length() == 0) { trashCode += "l"; } }
             
             if(trashCode.length() == 0){
@@ -1295,9 +1298,11 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
         
         if (uniques.size() != 0) {
             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
+                if (m->control_pressed) { break; }
                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
             }
             for (map<string, pairFastqRead>:: iterator it = pairUniques.begin(); it != pairUniques.end(); it++) {
+                if (m->control_pressed) { break; }
                 m->mothurOut("[WARNING]: did not find paired read for " + (it->first).substr(1) + ", ignoring.\n");
             }
             m->mothurOutEndLine();
@@ -1657,6 +1662,7 @@ fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
         
         vector<int> qualScores = convertQual(quality);
         
+        m->checkName(name);
         read.name = name;
         read.sequence = sequence;
         read.scores = qualScores;
@@ -1971,7 +1977,6 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, stri
                     else { uniquePrimers.insert(tempPair); }
                                        
                     if (m->debug) {  if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); }  }
-                    
                                        primers[indexPrimer]=newPrimer; indexPrimer++;          
                                        primerNameVector.push_back(group);
                                }else if(type == "BARCODE"){