X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.cpp;h=c664ad7548b52f8966c799749f382d31169f564d;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=0a2e9380ebd71a5deae50725d3b36c2d10b52c4e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 0a2e938..c664ad7 100644
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -66,6 +66,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -112,11 +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(); }
@@ -163,7 +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() != "") {
@@ -191,7 +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);
@@ -201,7 +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 = "";