X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=a90e7adc5c8cb870714c716b02bec5eb6bfddd73;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=3b9d195f34fa3e916ae9b3d92328195c1337579e;hpb=cbaa068e77aeb15bb06f0695a36d8f757977ed64;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 3b9d195..a90e7ad 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -607,11 +607,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 
 			Sequence currSeq(inFASTA); m->gobble(inFASTA);
 			//cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
-            if (m->debug) { m->mothurOut("[DEBUG]: " + toString(count) + " fasta = " + currSeq.getName() + '\n'); }
+            
 			QualityScores currQual;
 			if(qFileName != ""){
 				currQual = QualityScores(qFile);  m->gobble(qFile);
-                 if (m->debug) { m->mothurOut("[DEBUG]: qual = " + currQual.getName() + '\n'); }
+                //cout << currQual.getName() << endl;
 			}
 			
 			string origSeq = currSeq.getUnaligned();
@@ -883,6 +883,8 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
 								 tempNameFileNames,
 								 lines[process],
 								 qLines[process]);
+                
+                if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); }
 				
 				//pass groupCounts to parent
 				if(createGroup){
@@ -1253,7 +1255,9 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
 		while(!inOligos.eof()){
 
 			inOligos >> type; 
-		 			
+            
+		 	if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }	
+            
 			if(type[0] == '#'){
 				while (!inOligos.eof())	{	char c = inOligos.get();  if (c == 10 || c == 13){	break;	}	} // get rest of line if there's any crap there
 				m->gobble(inOligos);
@@ -1264,6 +1268,8 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
 				for(int i=0;i<type.length();i++){	type[i] = toupper(type[i]);  }
 				
 				inOligos >> oligo;
+                
+                if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
 				
 				for(int i=0;i<oligo.length();i++){
 					oligo[i] = toupper(oligo[i]);
@@ -1285,6 +1291,8 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
 					map<string, int>::iterator itPrime = primers.find(oligo);
 					if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 					
+                    if (m->debug) {  if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); }  }
+                    
 					primers[oligo]=indexPrimer; indexPrimer++;		
 					primerNameVector.push_back(group);
 				}
@@ -1309,15 +1317,22 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
 					
                     //then this is illumina data with 4 columns
                     if (temp != "") {  
-                        string reverseBarcode = reverseOligo(group); //reverse barcode
-                        group = temp;
                         
+                        for(int i=0;i<group.length();i++){
+                            group[i] = toupper(group[i]);
+                            if(group[i] == 'U')	{	group[i] = 'T';	}
+                        }
+                        
+                        if (m->debug) { m->mothurOut("[DEBUG]: reading reverse " + group + ", and group = " + temp + ".\n"); }
+                        
+                        string reverseBarcode = reverseOligo(group); //reverse barcode
                         //check for repeat barcodes
                         map<string, int>::iterator itBar = rbarcodes.find(reverseBarcode);
-                        if (itBar != rbarcodes.end()) { m->mothurOut("barcode " + reverseBarcode + " is in your oligos file already."); m->mothurOutEndLine();  }
-						
+                        if (itBar != rbarcodes.end()) { m->mothurOut("reverse barcode " + group + " is in your oligos file already."); m->mothurOutEndLine();  }
+                        
+                        group = temp;
                         rbarcodes[reverseBarcode]=indexBarcode; 
-                    }
+                    }else { if (m->debug) { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); } }
                         
 					//check for repeat barcodes
 					map<string, int>::iterator itBar = barcodes.find(oligo);
@@ -1330,7 +1345,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
 				}else if(type == "SPACER"){
 					spacer.push_back(oligo);
 				}
-				else{	m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
+				else{	m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
 			}
 			m->gobble(inOligos);
 		}	
@@ -1436,7 +1451,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
 				break;
 			}
 		}
-		
+
 		if (allBlank) {
 			m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
 			allFiles = false;