changes while testing

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 16d83de2596b9cf84ab4069789917878fa89559e..4128142448b8412314dc2b1d8ce057c6e8527519 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -24,7 +24,7 @@ vector<string> TrimSeqsCommand::setParameters(){
         CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
                CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig);
                CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxhomop);
-               CommandParameter pminlength("minlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pminlength);
+               CommandParameter pminlength("minlength", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pminlength);
                CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxlength);
                CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
                CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
@@ -256,7 +256,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
                        m->mothurConvert(temp, maxHomoP);  
 
-                       temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
+                       temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "1"; }
                        m->mothurConvert(temp, minLength); 
                        
                        temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
@@ -715,7 +715,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        int currentSeqsDiffs = 0;
 
                        Sequence currSeq(inFASTA); m->gobble(inFASTA);
-                       //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
+                       //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
             Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
             
                        QualityScores currQual; QualityScores savedQual;
@@ -745,7 +745,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                     }
                                        else{ currentSeqsDiffs += success;  }
                                }
-                               
+                               //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
                 if(numSpacers != 0){
                                        success = trimOligos->stripSpacer(currSeq, currQual);
                                        if(success > sdiffs)            {       trashCode += 's';       }
@@ -775,13 +775,13 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                     
                     int thisBarcodeIndex = 0;
                     int thisPrimerIndex = 0;
-                    
+                    //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl;
                     if(numBarcodes != 0){
                         thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
                         if(thisSuccess > bdiffs)               { thisTrashCode += "b"; }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
-                    
+                    //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl;
                     if(numFPrimers != 0){
                         thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, keepforward);
                         if(thisSuccess > pdiffs)               { thisTrashCode += "f"; }