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

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a2c8021a57f6f3f076c8d1c9be7353eb8cffff93..21de6ac1f01e7ed4719443ecb578c0b4b9dac7b8 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -380,16 +380,16 @@ int TrimSeqsCommand::execute(){
                                        if (fastaFileNames[i][j] != "") {
                                                if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
                                                        if(m->isBlank(fastaFileNames[i][j])){
-                                                               remove(fastaFileNames[i][j].c_str());
+                                                               m->mothurRemove(fastaFileNames[i][j]);
                                                                namesToRemove.insert(fastaFileNames[i][j]);
                                                        
                                                                if(qFileName != ""){
-                                                                       remove(qualFileNames[i][j].c_str());
+                                                                       m->mothurRemove(qualFileNames[i][j]);
                                                                        namesToRemove.insert(qualFileNames[i][j]);
                                                                }
                                                                
                                                                if(nameFile != ""){
-                                                                       remove(nameFileNames[i][j].c_str());
+                                                                       m->mothurRemove(nameFileNames[i][j]);
                                                                        namesToRemove.insert(nameFileNames[i][j]);
                                                                }
                                                        }else{  
@@ -428,7 +428,7 @@ int TrimSeqsCommand::execute(){
                        }
                }
                
-               if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0;     }
+               if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 
                //output group counts
                m->mothurOutEndLine();
@@ -439,7 +439,7 @@ int TrimSeqsCommand::execute(){
                }
                if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
                
-               if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0;     }
+               if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 
                //set fasta file as new current fastafile
                string current = "";
@@ -546,7 +546,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                if(qFileName != ""){
                                        qFile.close();
                                }
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); }
 
                                return 0;
                        }
@@ -556,11 +556,12 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        int currentSeqsDiffs = 0;
 
                        Sequence currSeq(inFASTA); m->gobble(inFASTA);
+                       //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
                        QualityScores currQual;
                        if(qFileName != ""){
                                currQual = QualityScores(qFile);  m->gobble(qFile);
                        }
-                       //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
+                       
                        string origSeq = currSeq.getUnaligned();
                        if (origSeq != "") {
                                
@@ -846,27 +847,27 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                        m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
                        
                        m->appendFiles((trimFASTAFileName + toString(processIDS[i]) + ".temp"), trimFASTAFileName);
-                       remove((trimFASTAFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((trimFASTAFileName + toString(processIDS[i]) + ".temp"));
                        m->appendFiles((scrapFASTAFileName + toString(processIDS[i]) + ".temp"), scrapFASTAFileName);
-                       remove((scrapFASTAFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((scrapFASTAFileName + toString(processIDS[i]) + ".temp"));
                        
                        if(qFileName != ""){
                                m->appendFiles((trimQualFileName + toString(processIDS[i]) + ".temp"), trimQualFileName);
-                               remove((trimQualFileName + toString(processIDS[i]) + ".temp").c_str());
+                               m->mothurRemove((trimQualFileName + toString(processIDS[i]) + ".temp"));
                                m->appendFiles((scrapQualFileName + toString(processIDS[i]) + ".temp"), scrapQualFileName);
-                               remove((scrapQualFileName + toString(processIDS[i]) + ".temp").c_str());
+                               m->mothurRemove((scrapQualFileName + toString(processIDS[i]) + ".temp"));
                        }
                        
                        if(nameFile != ""){
                                m->appendFiles((trimNameFileName + toString(processIDS[i]) + ".temp"), trimNameFileName);
-                               remove((trimNameFileName + toString(processIDS[i]) + ".temp").c_str());
+                               m->mothurRemove((trimNameFileName + toString(processIDS[i]) + ".temp"));
                                m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
-                               remove((scrapNameFileName + toString(processIDS[i]) + ".temp").c_str());
+                               m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
                        }
                        
                        if(oligoFile != ""){
                                m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
-                               remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+                               m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
                        }
                        
                        
@@ -875,16 +876,16 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                        for(int k=0;k<fastaFileNames[j].size();k++){
                                                if (fastaFileNames[j][k] != "") {
                                                        m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
-                                                       remove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+                                                       m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
                                                        
                                                        if(qFileName != ""){
                                                                m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
-                                                               remove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+                                                               m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
                                                        }
                                                        
                                                        if(nameFile != ""){
                                                                m->appendFiles((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"), nameFileNames[j][k]);
-                                                               remove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+                                                               m->mothurRemove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"));
                                                        }
                                                }
                                        }
@@ -909,7 +910,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                                else { groupCounts[it->first] += tempNum; }
                                        }
                                }
-                               in.close(); remove(tempFile.c_str());
+                               in.close(); m->mothurRemove(tempFile);
                        }
                        
                }