modified reverse.seqs and qualscores.cpp

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index d2c0fcb64f92652a14dee26e40e89ae5dc9a19dd..b31c4e0d89ecdb7243e9f4e42d3dc0af1d903450 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -27,8 +27,7 @@ vector<string> SeqErrorCommand::getValidParameters(){
 //**********************************************************************************************************************
 SeqErrorCommand::SeqErrorCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["error.summary"] = tempOutNames;
                outputTypes["error.seq"] = tempOutNames;
@@ -73,10 +72,10 @@ vector<string> SeqErrorCommand::getRequiredFiles(){
 SeqErrorCommand::SeqErrorCommand(string option)  {
        try {
                
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        string temp;
@@ -231,7 +230,7 @@ SeqErrorCommand::~SeqErrorCommand(){
 
 int SeqErrorCommand::execute(){
        try{
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
                string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
                m->openOutputFile(errorSummaryFileName, errorSummaryFile);
@@ -344,7 +343,7 @@ int SeqErrorCommand::execute(){
                                int startBase = report.getQueryStart();
                                int endBase = report.getQueryEnd();
 
-                               quality = QualityScores(qualFile, origLength);
+                               quality = QualityScores(qualFile);
 
                                if(!ignoreSeq){
                                        quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
@@ -506,7 +505,7 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
                                if(started == 1){       break;  }
                        }
                        else if(q[i] != '.' && r[i] == '.'){            //      query extends beyond reference
-                               m->mothurOut("Warning: " + toString(query.getName()) + " extend beyond " + toString(reference.getName()) + ".  Ignoring the extra bases in the query\n");
+//                             m->mothurOut("Warning: " + toString(query.getName()) + " extend beyond " + toString(reference.getName()) + ".  Ignoring the extra bases in the query\n");
                                if(started == 1){       break;  }
                        }
                        else if(q[i] == '.' && r[i] == '.'){            //      both are missing data