X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=3718c9a9c0cf843d9f91311b8b7b3cdee814f455;hb=4a760c2d164aa955dee7d3d38da323822763d906;hp=51495506c6e7a3303c6a87d0510a87e44f1810f6;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a;p=mothur.git

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 5149550..3718c9a 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -294,7 +294,8 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
             
             summaryfile = validParameter.validFile(parameters, "summary", true);
 			if (summaryfile == "not open") { summaryfile = ""; abort = true; }
-			else if (summaryfile == "not found") { summaryfile = "";  }	
+			else if (summaryfile == "not found") { summaryfile = "";  }
+            else { m->setSummaryFile(summaryfile); }
             
             if ((namefile != "") && (countfile != "")) {
                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
@@ -1080,8 +1081,6 @@ int ScreenSeqsCommand::screenNameGroupFile(map<string, string> badSeqNames){
 			it = badSeqNames.find(seqName);
 				
 			if(it != badSeqNames.end()){
-				badSeqNames.erase(it);
-				
 				if(namefile != ""){
 					int start = 0;
 					for(int i=0;i<seqList.length();i++){
@@ -1092,6 +1091,7 @@ int ScreenSeqsCommand::screenNameGroupFile(map<string, string> badSeqNames){
 					}
 					badSeqGroups[seqList.substr(start,seqList.length()-start)] = it->second;
 				}
+                badSeqNames.erase(it);
 			}
 			else{
 				goodNameOut << seqName << '\t' << seqList << endl;
@@ -2302,7 +2302,7 @@ int ScreenSeqsCommand::screenQual(map<string, string> badSeqNames){
 				saveName = name.substr(1);
 				while (!in.eof())	{	
 					char c = in.get(); 
-					if (c == 10 || c == 13){	break;	}
+					if (c == 10 || c == 13 || c == -1){	break;	}
 					else { name += c; }	
 				} 
 				m->gobble(in);