X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=051aa99434f6bb21a8d3b3b54cb2cc671eab98d2;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=51495506c6e7a3303c6a87d0510a87e44f1810f6;hpb=eb71e28b7b7afd82540f4a8f0bac9429c5b9d713;p=mothur.git

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 5149550..051aa99 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;
@@ -682,7 +683,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 nameMap = ct.getNameMap();
             }
             getSummary(positions); 
@@ -713,7 +714,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 nameMap = ct.getNameMap();
             }
             getSummaryReport();
@@ -1018,7 +1019,7 @@ int ScreenSeqsCommand::screenFasta(map<string, string>& badSeqNames){
 			if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 nameMap = ct.getNameMap();
             }
 			getSummary(positions); 
@@ -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;
@@ -2206,7 +2206,7 @@ int ScreenSeqsCommand::screenCountFile(map<string, string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile);
+            ct.readTable(goodCountFile, true);
             ct.printTable(goodCountFile);
         }
 		
@@ -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);
@@ -2409,10 +2409,10 @@ int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccn
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+			if((count) % 100 == 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); 		}
 		}
 		//report progress
-		if((count) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+		if((count) % 100 != 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); 	}
 		
 			
 		goodFile.close();
@@ -2504,7 +2504,7 @@ int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File&
 			}
 			
 			//report progress
-			if((i) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();		}
+			if((i) % 100 == 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(i)+"\n"); 		}
 		}
 				
 		return 1;