some of pat's small modifications

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 6ee865516bee6851fadf28f81e70bb249c35562d..bcf996b53a1f2cd385fa7bb00a2c2c7c50cf4343 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -18,8 +18,6 @@ vector<string> TrimFlowsCommand::setParameters(){
                CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
                CommandParameter pmaxflows("maxflows", "Number", "", "720", "", "", "",false,false); parameters.push_back(pmaxflows);
                CommandParameter pminflows("minflows", "Number", "", "360", "", "", "",false,false); parameters.push_back(pminflows);
-               CommandParameter pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
-               CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
                CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
                CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
                CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
@@ -172,13 +170,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 
                        temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
                        convert(temp, noise);  
-
-                       temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found"){       temp = "0";             }
-                       convert(temp, minLength); 
-                       
-                       temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found"){       temp = "0";             }
-                       convert(temp, maxLength);
-                       
+       
                        temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
                        convert(temp, bdiffs);
                        
@@ -190,9 +182,6 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        convert(temp, tdiffs);
                        if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
                        
-                       temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found"){ temp = "T";           }
-                       allFiles = m->isTrue(temp);
-                       
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        convert(temp, processors);
@@ -203,7 +192,8 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                                m->mothurOut("The value of the order option must be four bases long\n");
                        }
 
-                       if(oligoFileName == ""){        allFiles = 0;           }
+                       if(oligoFileName == "") {       allFiles = 0;           }
+                       else                                    {       allFiles = 1;           }
 
                        numFPrimers = 0;
                        numRPrimers = 0;
@@ -380,14 +370,6 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                                trashCode += 'l';
                        }
                        
-                       if(minLength > 0 || maxLength > 0){     //screen to see if sequence is above and below a specific number of bases
-                               int seqLength = currSeq.getNumBases();
-                               if(seqLength < minLength || seqLength > maxLength){
-                                       success = 0;
-                                       trashCode += 'l';
-                               }
-                       }
-                       
                        int primerIndex = 0;
                        int barcodeIndex = 0;