X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=a56b0ebb73d1f6188ecd09430e70ed0128abaf31;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=e7b2c6acedf523f8249c8159ed186a6b8d5b8892;hpb=d39c47623faf0dc1e271f3d50efa6b029b622b88;p=mothur.git

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index e7b2c6a..a56b0eb 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -14,7 +14,7 @@
 vector<string> ScreenSeqsCommand::setParameters(){	
 	try {
 		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
-        CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "report", "none", "none","contigsreport",false,true,true); parameters.push_back(pcontigsreport);
+        CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "report", "none", "none","contigsreport",false,false,true); parameters.push_back(pcontigsreport);
         CommandParameter palignreport("alignreport", "InputTypes", "", "", "report", "none", "none","alignreport",false,false); parameters.push_back(palignreport);
         CommandParameter psummary("summary", "InputTypes", "", "", "report", "none", "none","summary",false,false); parameters.push_back(psummary);
         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
@@ -683,7 +683,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 nameMap = ct.getNameMap();
             }
             getSummary(positions); 
@@ -714,7 +714,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 nameMap = ct.getNameMap();
             }
             getSummaryReport();
@@ -1019,7 +1019,7 @@ int ScreenSeqsCommand::screenFasta(map<string, string>& badSeqNames){
 			if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 nameMap = ct.getNameMap();
             }
 			getSummary(positions); 
@@ -2177,19 +2177,18 @@ int ScreenSeqsCommand::screenCountFile(map<string, string> badSeqNames){
 			if (m->control_pressed) { goodCountOut.close(); in.close(); m->mothurRemove(goodCountFile); return 0; }
             
 			in >> name; m->gobble(in); 
-            in >> thisTotal; m->gobble(in);
+            in >> thisTotal; 
             rest = m->getline(in); m->gobble(in);
             
 			it = badSeqNames.find(name);
 			
 			if(it != badSeqNames.end()){
-				badSeqNames.erase(it);
+				badSeqNames.erase(it); 
 			}
 			else{
 				goodCountOut << name << '\t' << thisTotal << '\t' << rest << endl;
 			}
 		}
-		
 		if (m->control_pressed) { goodCountOut.close();  in.close(); m->mothurRemove(goodCountFile);  return 0; }
         
 		//we were unable to remove some of the bad sequences
@@ -2206,7 +2205,7 @@ int ScreenSeqsCommand::screenCountFile(map<string, string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile, true);
+            ct.readTable(goodCountFile, true, false);
             ct.printTable(goodCountFile);
         }