X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=cbf5e13603ced805d185196fad9129eacb573d22;hb=bc4c4d63e983a3e91e74b5038bfec6705e1a3a2e;hp=944e2cdc0a110828157301f14f2470a06ac3e052;hpb=a86aff4f80701bf0d436f02c0095920114e1cba2;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 944e2cd..cbf5e13 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -283,6 +283,7 @@ int TrimSeqsCommand::execute(){
 										
 		for(int i=0;i<fastaFileNames.size();i++){
 			if (isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
+			else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
 			else {
 				ifstream inFASTA;
 				string seqName;
@@ -443,7 +444,6 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 							}
 						}
 						outGroups << currSeq.getName() << '\t' << thisGroup << endl;
-						
 						if(allFiles){
 							currSeq.printSequence(*fastaFileNames[indexToFastaFile]);					
 						}
@@ -583,11 +583,14 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
 		
 		while(!inOligos.eof()){
 			inOligos >> type;
-			
+		 			
 			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
 			}
 			else{
+				//make type case insensitive
+				for(int i=0;i<type.length();i++){	type[i] = toupper(type[i]);  }
+				
 				inOligos >> oligo;
 				
 				for(int i=0;i<oligo.length();i++){
@@ -595,7 +598,7 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
 					if(oligo[i] == 'U')	{	oligo[i] = 'T';	}
 				}
 				
-				if(type == "forward"){
+				if(type == "FORWARD"){
 					group = "";
 					
 					// get rest of line in case there is a primer name
@@ -614,18 +617,21 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
 					groupVector.push_back(group);
 					
 					if(allFiles){
-						if (group != "") { //there is a group for this primer
+						outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
+						if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
+							filesToRemove.insert((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
+						}else {
 							outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
-							outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
 						}
 					}
+
 				}
-				else if(type == "reverse"){
+				else if(type == "REVERSE"){
 					Sequence oligoRC("reverse", oligo);
 					oligoRC.reverseComplement();
 					revPrimer.push_back(oligoRC.getUnaligned());
 				}
-				else if(type == "barcode"){
+				else if(type == "BARCODE"){
 					inOligos >> group;
 					
 					//check for repeat barcodes