X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=4128142448b8412314dc2b1d8ce057c6e8527519;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=ec136dbe7eb02df1a659111766c5bff8bfc22222;hpb=75cff1a83a64cd46e9dd603e02597a2bb6a76119;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index ec136db..4128142 100644
--- 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);
@@ -443,7 +443,9 @@ int TrimSeqsCommand::execute(){
 				outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
 			}
 		}
-       
+        
+        if (!pairedOligos) { if (reorient) { m->mothurOut("[WARNING]: You cannot use reorient without paired barcodes or primers, skipping."); m->mothurOutEndLine(); reorient = false; } }
+        
         if (m->control_pressed) { return 0; }
             
         //fills lines and qlines
@@ -538,7 +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;
                 
@@ -713,7 +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;
@@ -738,10 +740,12 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                 
 				if(numBarcodes != 0){
 					success = trimOligos->stripBarcode(currSeq, currQual, barcodeIndex);
-					if(success > bdiffs)		{	trashCode += 'b';	}
+					if(success > bdiffs)		{
+                        trashCode += 'b';
+                    }
 					else{ currentSeqsDiffs += success;  }
 				}
-				
+				//cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
                 if(numSpacers != 0){
 					success = trimOligos->stripSpacer(currSeq, currQual);
 					if(success > sdiffs)		{	trashCode += 's';	}
@@ -752,9 +756,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 				if(numFPrimers != 0){
 					success = trimOligos->stripForward(currSeq, currQual, primerIndex, keepforward);
 					if(success > pdiffs)		{
-                        //if (pairedOligos) {  trashCode += trimOligos->getTrashCode(); }
-                        //else {  trashCode += 'f';  }
-                        trashCode += 'f';
+                          trashCode += 'f';  
                     }
 					else{ currentSeqsDiffs += success;  }
 				}
@@ -773,20 +775,16 @@ 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';	}
+                        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)		{
-                            //if (pairedOligos) {  thisTrashCode += rtrimOligos->getTrashCode(); }
-                            //else {  thisTrashCode += 'f';  }
-                            thisTrashCode += 'f'; 
-                        }
+                        if(thisSuccess > pdiffs)		{ thisTrashCode += "f"; }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
                    
@@ -804,7 +802,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                             savedQual.flipQScores();
                             currQual.setScores(savedQual.getScores());
                         }
-                    }
+                    }else { trashCode += "(" + thisTrashCode + ")";  }
                 }
                 
 				if(keepFirst != 0){
@@ -1393,9 +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);
                         
@@ -1535,7 +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;  }
 					} 
@@ -1650,10 +1646,10 @@ 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;	}
-		
+        
 		//add in potential combos
 		if(barcodeNameVector.size() == 0){
 			barcodes[""] = 0;