X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makecontigscommand.cpp;h=72e8ea09aeeac366fc08175dd7019e404020835d;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=87027f4df5e0166f25852fec44cd6cfa120c90a7;hpb=a935b75dd890da5ae7f09e5e6179f90ab2955348;p=mothur.git

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index 87027f4..72e8ea0 100644
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -704,7 +704,7 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
 					for(int i=0;i<tempFASTAFileNames.size();i++){
 						for(int j=0;j<tempFASTAFileNames[i].size();j++){
 							if (tempFASTAFileNames[i][j] != "") {
-								tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
+								tempFASTAFileNames[i][j] += m->mothurGetpid(process) + ".temp";
 								m->openOutputFile(tempFASTAFileNames[i][j], temp);			temp.close();
 							}
 						}
@@ -712,14 +712,14 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
 				}
                 
 				num = driver(files[process], 
-                             outputFasta + toString(getpid()) + ".temp", 
-                             outputScrapFasta + toString(getpid()) + ".temp", 
-                             outputMisMatches + toString(getpid()) + ".temp",
+                             outputFasta + m->mothurGetpid(process) + ".temp",
+                             outputScrapFasta + m->mothurGetpid(process) + ".temp",
+                             outputMisMatches + m->mothurGetpid(process) + ".temp",
                              tempFASTAFileNames, process, group);
 				
 				//pass groupCounts to parent
                 ofstream out;
-                string tempFile = toString(getpid()) + ".num.temp";
+                string tempFile = m->mothurGetpid(process) + ".num.temp";
                 m->openOutputFile(tempFile, out);
                 out << num << endl;
 				if (createFileGroup || createOligosGroup) {
@@ -1143,7 +1143,7 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
             num++;
             
 			//report progress
-			if((num) % 1000 == 0){	m->mothurOut(toString(num)); m->mothurOutEndLine();		}
+			if((num) % 1000 == 0){	m->mothurOutJustToScreen(toString(num)); m->mothurOutEndLine();		}
 		}
         
 		//report progress
@@ -1289,7 +1289,7 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
                     count++;
                     
                     //report progress
-                    if((count) % 10000 == 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+                    if((count) % 10000 == 0){	m->mothurOutJustToScreen(toString(count)); m->mothurOutEndLine();		}
                 //}
             }
 		}
@@ -1298,9 +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();
@@ -1660,6 +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;
@@ -1974,7 +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"){