rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / degapseqscommand.cpp

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index f590d8b3baaf67091f59a741a87a23e09c8873b0..1d83f3bef00d08574a66d7e5ecf21efa148452a4 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -197,7 +197,7 @@ int DegapSeqsCommand::execute(){
                        m->openOutputFile(degapFile, outFASTA);
                        
                        while(!inFASTA.eof()){
-                               if (m->control_pressed) {   outputTypes.clear(); inFASTA.close();  outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } return 0; }
+                               if (m->control_pressed) {   outputTypes.clear(); inFASTA.close();  outFASTA.close(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]);        } return 0; }
                                 
                                Sequence currSeq(inFASTA);  m->gobble(inFASTA);
                                if (currSeq.getName() != "") {
@@ -210,7 +210,7 @@ int DegapSeqsCommand::execute(){
                        
                        outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile);
                        
-                       if (m->control_pressed) {  outputTypes.clear(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); } return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) {      m->mothurRemove(outputNames[j]);        } return 0; }
                }
                
                //set fasta file as new current fastafile