X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqerrorcommand.cpp;h=5879241372dd3b60b34683683a0c1edbcbd64d57;hp=00897dcfee5881be8dfd37d00bbbe705a3d034f3;hb=615301e57c25e241356a9c2380648d117709458d;hpb=859e3a473a3e63e0060c49be70b80f9289253da2

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 00897dc..5879241 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -358,7 +358,7 @@ int SeqErrorCommand::execute(){
 		if(namesFileName != "")     {	weights = getWeights();         }
         else if (countfile != "")   {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             weights = ct.getNameMap();
         }
 		
@@ -666,7 +666,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
 			int misMatchSize;
 			in >> misMatchSize; m->gobble(in);
 			if (misMatchSize > misMatchCounts.size()) {	misMatchCounts.resize(misMatchSize, 0);	}
-			for (int j = 0; j < misMatchCounts.size(); j++) {
+			for (int j = 0; j < misMatchSize; j++) {
 				in >> tempNum; misMatchCounts[j] += tempNum;
 			}
 			m->gobble(in);
@@ -881,7 +881,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 				if (queryFile.eof()) { break; }
 			#endif
 			
-			if(index % 100 == 0){	m->mothurOut(toString(index));	m->mothurOutEndLine(); }
+			if(index % 100 == 0){	m->mothurOutJustToScreen(toString(index)+"\n");	 }
 		}
 		queryFile.close();
 		outChimeraReport.close();
@@ -892,7 +892,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 		else if(qFileName != "" && aligned == false){   qualFile.close();                       }
         
 		//report progress
-		m->mothurOut(toString(index));	m->mothurOutEndLine();
+		m->mothurOutJustToScreen(toString(index)+"\n");	
 		
 		return index;
 	}
@@ -1412,9 +1412,7 @@ 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; }
-                    }
+                    m->checkName(sname);
 					
 					map<string, int>::iterator it = firstSeqNames.find(sname);
 					
@@ -1475,9 +1473,7 @@ 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; }
-                    }
+                    m->checkName(sname);
                     
                     map<string, int>::iterator it = firstSeqNamesReport.find(sname);