paralellized the indicator command

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6410c8f4cb39a32efad1f8a18e4876cec6080b9f..a2c8021a57f6f3f076c8d1c9be7353eb8cffff93 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -189,6 +189,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                                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 if (fastaFile == "not open") { abort = true; }    
+                       else { m->setFastaFile(fastaFile); }
                        
                        //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"){  
@@ -207,7 +208,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "oligos", true);
                        if (temp == "not found"){       oligoFile = "";         }
                        else if(temp == "not open"){    abort = true;   } 
-                       else                                    {       oligoFile = temp;               }
+                       else                                    {       oligoFile = temp; m->setOligosFile(oligoFile);          }
                        
                        
                        temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
@@ -236,12 +237,12 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "qfile", true);     
                        if (temp == "not found")        {       qFileName = "";         }
                        else if(temp == "not open")     {       abort = true;           }
-                       else                                            {       qFileName = temp;       }
+                       else                                            {       qFileName = temp;       m->setQualFile(qFileName); }
                        
                        temp = validParameter.validFile(parameters, "name", true);      
                        if (temp == "not found")        {       nameFile = "";          }
                        else if(temp == "not open")     {       nameFile = "";  abort = true;           }
-                       else                                            {       nameFile = temp;        }
+                       else                                            {       nameFile = temp;        m->setNameFile(nameFile); }
                        
                        temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
                        convert(temp, qThreshold);
@@ -603,7 +604,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                        else if(qRollAverage != 0)      {       success = currQual.stripQualRollingAverage(currSeq, qRollAverage);      }
                                        else if(qWindowAverage != 0){   success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);   }
                                        else                                            {       success = 1;                            }
-                               
+                                       
                                        //you don't want to trim, if it fails above then scrap it
                                        if ((!qtrim) && (origLength != currSeq.getNumBases())) {  success = 0; }