forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / makefastqcommand.cpp

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index 2dd45a542665c71a1221adca4eed77d9c1bb65f5..0f6e030bb0d1fec3f7cf99614fa0827c66de2bb5 100644 (file)
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -116,7 +116,7 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastafile); }   
                        
                        qualfile = validParameter.validFile(parameters, "qfile", true);
                        if (qualfile == "not open") { abort = true; qualfile = ""; }
@@ -124,7 +124,7 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
                                qualfile = m->getQualFile(); 
                                if (qualfile != "") {  m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setQualFile(qualfile); }     
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);              }
@@ -181,7 +181,7 @@ int MakeFastQCommand::execute(){
                qFile.close();
                out.close();
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -201,7 +201,7 @@ string MakeFastQCommand::convertQual(vector<int> qual) {
        try {
                string qualScores;
                
-               int controlChar = int('!');
+               int controlChar = int('@');
                
                for (int i = 0; i < qual.size(); i++) { 
                        int temp = qual[i] + controlChar;