X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.cpp;h=c664ad7548b52f8966c799749f382d31169f564d;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=17924c9669b6b5338d15824b2920410fcf305af4;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 17924c9..c664ad7 100644
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -113,11 +113,13 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
 			fastaFileName = validParameter.validFile(parameters, "fasta", true);
 			if (fastaFileName == "not open") { abort = true; }
 			else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }	
+			else { m->setFastaFile(fastaFileName); }
 			
 			qualFileName = validParameter.validFile(parameters, "qfile", true);
 			if (qualFileName == "not open") { abort = true; }
 			else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }	
-
+			else { m->setQualFile(qualFileName); }
+			
 			if((fastaFileName == "") && (qualFileName == "")){
 				fastaFileName = m->getFastaFile(); 
 				if (fastaFileName != "") {  m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
@@ -164,7 +166,7 @@ int ReverseSeqsCommand::execute(){
 			m->openOutputFile(fastaReverseFileName, outFASTA);
 			
 			while(!inFASTA.eof()){
-				if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(fastaReverseFileName.c_str()); return 0; }
+				if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
 				 
 				Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 				if (currSeq.getName() != "") {
@@ -192,7 +194,7 @@ int ReverseSeqsCommand::execute(){
 			m->openOutputFile(qualReverseFileName, outQual);
 
 			while(!inQual.eof()){
-				if (m->control_pressed) {  inQual.close();  outQual.close(); remove(qualReverseFileName.c_str()); return 0; }
+				if (m->control_pressed) {  inQual.close();  outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
 				currQual = QualityScores(inQual);  m->gobble(inQual);
 				currQual.flipQScores();	
 				currQual.printQScores(outQual);
@@ -202,7 +204,7 @@ int ReverseSeqsCommand::execute(){
 			outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
 		}
 		
-		if (m->control_pressed) {  remove(qualReverseFileName.c_str()); remove(fastaReverseFileName.c_str()); return 0; }
+		if (m->control_pressed) {  m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
 		
 		//set fasta file as new current fastafile
 		string current = "";