changes while testing

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a103626f7dd9fbed1074f7132175651360bfe464..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"; }
@@ -422,7 +422,7 @@ int TrimSeqsCommand::execute(){
                
                if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, true);
             nameCount = ct.getNameMap();
                        outputNames.push_back(trimCountFile);
                        outputNames.push_back(scrapCountFile);
@@ -540,7 +540,7 @@ int TrimSeqsCommand::execute(){
             
             if (countfile != "") { //create countfile with group info included
                 CountTable* ct = new CountTable();
-                ct->readTable(trimCountFile);
+                ct->readTable(trimCountFile, true);
                 map<string, int> justTrimmedNames = ct->getNameMap();
                 delete ct;
                 
@@ -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"; }
@@ -1391,9 +1391,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                         string sname = "";  nameStream >> sname;
                         sname = sname.substr(1);
                         
-                        for (int i = 0; i < sname.length(); i++) {
-                            if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
-                        }
+                        m->checkName(sname);
                         
                         map<string, int>::iterator it = firstSeqNames.find(sname);
                         
@@ -1533,7 +1531,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.get(); 
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 
@@ -1648,7 +1646,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
         if (hasPairedBarcodes || hasPrimer) {
             pairedOligos = true;
             if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true;  m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine();  return 0; }
-        }
+        }else if (reorient) { m->mothurOut("[Warning]: cannot use checkorient without paired barcodes or primers, ignoring.\n"); m->mothurOutEndLine(); reorient = false; }
         
                if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }