started work on sffinfo command. fixed bug across all paralellized commands if the...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index cbf5e13603ced805d185196fad9129eacb573d22..af3bfc8fcbf5ee10cb1a50b192ff414063bd740e 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -519,7 +519,7 @@ int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
                
                lines.clear();
                
-               vector<long int> positions;
+               vector<unsigned long int> positions;
                
                ifstream inFASTA;
                openInputFile(filename, inFASTA);
@@ -529,7 +529,7 @@ int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
                        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();
@@ -537,7 +537,7 @@ int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
                int numFastaSeqs = positions.size();
        
                FILE * pFile;
-               long size;
+               unsigned long int size;
                
                //get num bytes in file
                pFile = fopen (filename.c_str(),"rb");
@@ -552,11 +552,11 @@ int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
                
                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;
                        }else{  
-                               long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
+                               unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
                        }
                        lines.push_back(new linePair(startPos, numSeqsPerProcessor));
                }