X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=screenseqscommand.cpp;h=bf702e13534f507576bee7c24bcf6462aacb7ca3;hp=e40c41218f5a599d894e0b2cb52f54406635f9ee;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index e40c412..bf702e1 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); 
@@ -2119,7 +2119,7 @@ int ScreenSeqsCommand::screenGroupFile(map<string, string> badSeqNames){
 		while(!inputGroups.eof()){
 			if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; }
 
-			inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group;
+			inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group; m->gobble(inputGroups);
 			it = badSeqNames.find(seqName);
 			
 			if(it != badSeqNames.end()){
@@ -2128,7 +2128,6 @@ int ScreenSeqsCommand::screenGroupFile(map<string, string> badSeqNames){
 			else{
 				goodGroupOut << seqName << '\t' << group << endl;
 			}
-			m->gobble(inputGroups);
 		}
 		
 		if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); m->mothurRemove(goodGroupFile);  return 0; }
@@ -2205,7 +2204,7 @@ 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);
         }