X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=ecd6f0ceb723290337f5856f724710eff7a751ee;hb=7d9e2bc58855132983da7ac9342880bc95055f77;hp=67e43aa0d4b7f6a6ff251bc45a8254ca49b8b162;hpb=20071b183e619c122bf9f63b4bb42722507c4e4a;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 67e43aa..ecd6f0c 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -407,6 +407,13 @@ int SeqErrorCommand::execute(){
 		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");
 		m->mothurOutEndLine();
 		
+        //set fasta file as new current fastafile
+		string current = "";
+		itTypes = outputTypes.find("errorseq");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+		}
+        
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
@@ -673,10 +680,10 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 		int numSeqs = 0;
 		
 		map<string, int>::iterator it;
-		qScoreErrorMap['m'].assign(41, 0);
-		qScoreErrorMap['s'].assign(41, 0);
-		qScoreErrorMap['i'].assign(41, 0);
-		qScoreErrorMap['a'].assign(41, 0);
+		qScoreErrorMap['m'].assign(101, 0);
+		qScoreErrorMap['s'].assign(101, 0);
+		qScoreErrorMap['i'].assign(101, 0);
+		qScoreErrorMap['a'].assign(101, 0);
 		
 		errorForward['m'].assign(maxLength,0);
 		errorForward['s'].assign(maxLength,0);
@@ -712,8 +719,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 			qualForwardMap.resize(maxLength);
 			qualReverseMap.resize(maxLength);
 			for(int i=0;i<maxLength;i++){
-				qualForwardMap[i].assign(41,0);
-				qualReverseMap[i].assign(41,0);
+				qualForwardMap[i].assign(101,0);
+				qualReverseMap[i].assign(101,0);
 			}	
 		}
 		else if(qFileName != "" && !aligned){
@@ -724,8 +731,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 			qualForwardMap.resize(maxLength);
 			qualReverseMap.resize(maxLength);
 			for(int i=0;i<maxLength;i++){
-				qualForwardMap[i].assign(41,0);
-				qualReverseMap[i].assign(41,0);
+				qualForwardMap[i].assign(101,0);
+				qualReverseMap[i].assign(101,0);
 			}	
         }
         
@@ -1271,7 +1278,7 @@ void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
 		outputNames.push_back(errorQualityFileName);  outputTypes["errorquality"].push_back(errorQualityFileName);
 
 		errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
-		for(int i=0;i<41;i++){
+		for(int i=0;i<101;i++){
 			errorQualityFile << i << '\t' << qScoreErrorMap['m'][i] << '\t' << qScoreErrorMap['s'][i] << '\t' << qScoreErrorMap['i'][i] << '\t'<< qScoreErrorMap['a'][i] << endl;
 		}
 		errorQualityFile.close();
@@ -1381,6 +1388,10 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 					
 					string sname = "";  nameStream >> sname;
 					sname = sname.substr(1);
+                    
+                    for (int i = 0; i < sname.length(); i++) {
+                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+                    }
 					
 					map<string, int>::iterator it = firstSeqNames.find(sname);
 					
@@ -1441,6 +1452,10 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                     istringstream nameStream(input);
                     string sname = "";  nameStream >> sname;
                     
+                    for (int i = 0; i < sname.length(); i++) {
+                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+                    }
+                    
                     map<string, int>::iterator it = firstSeqNamesReport.find(sname);
                 
                     if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk