pat's changes to trim.seqs

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 1f93068d6451d701d6587b7b913bcc0e0856fd90..8d1b40f37cd7eb9edfc708e3b9e856092de5eb5a 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -267,26 +267,14 @@ int AlignCommand::execute(){
                                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                                int inMode=MPI_MODE_RDONLY; 
                                
-                               //char* outAlignFilename = new char[alignFileName.length()];
-                               //memcpy(outAlignFilename, alignFileName.c_str(), alignFileName.length());
-                               
                                char outAlignFilename[1024];
                                strcpy(outAlignFilename, alignFileName.c_str());
-
-                               //char* outReportFilename = new char[reportFileName.length()];
-                               //memcpy(outReportFilename, reportFileName.c_str(), reportFileName.length());
                                
                                char outReportFilename[1024];
                                strcpy(outReportFilename, reportFileName.c_str());
-
-                               //char* outAccnosFilename = new char[accnosFileName.length()];
-                               //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
                                
                                char outAccnosFilename[1024];
                                strcpy(outAccnosFilename, accnosFileName.c_str());
-
-                               //char* inFileName = new char[candidateFileNames[s].length()];
-                               //memcpy(inFileName, candidateFileNames[s].c_str(), candidateFileNames[s].length());
                                
                                char inFileName[1024];
                                strcpy(inFileName, candidateFileNames[s].c_str());
@@ -398,7 +386,7 @@ int AlignCommand::execute(){
                                }
                        }
                        else{
-                               vector<int> positions;
+                               vector<unsigned long int> positions;
                                processIDS.resize(0);
                                
                                ifstream inFASTA;
@@ -408,7 +396,7 @@ int AlignCommand::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();
@@ -418,7 +406,7 @@ int AlignCommand::execute(){
                                int numSeqsPerProcessor = numFastaSeqs / 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 = numFastaSeqs - i * numSeqsPerProcessor;
                                        }