]> git.donarmstrong.com Git - mothur.git/blobdiff - chimerapintailcommand.cpp
pat's slight modifications to trim.seqs
[mothur.git] / chimerapintailcommand.cpp
index 6cf581b9308f21159186ece928bcbdf8e4142803..fa7fd170fb15cd4f224df0094b139dd24c93c88d 100644 (file)
@@ -91,7 +91,17 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                                if (pid == 0) {
                                        #endif
 
-                                       ableToOpen = openInputFile(fastaFileNames[i], in);
+                                       ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+                               
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getDefaultPath() != "") { //default path is set
+                                                       string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       fastaFileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        #ifdef USE_MPI  
@@ -106,7 +116,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                        #endif
 
                                        if (ableToOpen == 1) { 
-                                               m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
                                                //erase from file list
                                                fastaFileNames.erase(fastaFileNames.begin()+i);
                                                i--;
@@ -359,7 +369,7 @@ int ChimeraPintailCommand::execute(){
                                        }
                                        
                                }else{
-                                       vector<int> positions;
+                                       vector<unsigned long int> positions;
                                        processIDS.resize(0);
                                        
                                        ifstream inFASTA;
@@ -369,7 +379,7 @@ int ChimeraPintailCommand::execute(){
                                        while(!inFASTA.eof()){
                                                input = getline(inFASTA);
                                                if (input.length() != 0) {
-                                                       if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
+                                                       if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
                                                }
                                        }
                                        inFASTA.close();
@@ -379,7 +389,7 @@ int ChimeraPintailCommand::execute(){
                                        int numSeqsPerProcessor = numSeqs / processors;
                                        
                                        for (int i = 0; i < processors; i++) {
-                                               long int startPos = positions[ i * numSeqsPerProcessor ];
+                                               unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
                                                if(i == processors - 1){
                                                        numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
                                                }