fixes while testing 1.33.0

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index e7b2c6acedf523f8249c8159ed186a6b8d5b8892..bf702e13534f507576bee7c24bcf6462aacb7ca3 100644 (file)
--- 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; }
@@ -2177,19 +2176,18 @@ 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 +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);
         }