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

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 6c5d827d6553eac7f8ca8696091dd3ab7c87e4f3..2a210b01ad3a8fb0812c1877595028a851bdbee7 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -478,7 +478,7 @@ int ClassifySeqsCommand::execute(){
                                driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
                        }
                        else{
-                               vector<int> positions;
+                               vector<unsigned long int> positions;
                                processIDS.resize(0);
                                
                                ifstream inFASTA;
@@ -488,7 +488,7 @@ int ClassifySeqsCommand::execute(){
                                while(!inFASTA.eof()){
                                        input = getline(inFASTA);
                                        if (input.length() != 0) {
-                                               if(input[0] == '>'){    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();
@@ -496,9 +496,9 @@ int ClassifySeqsCommand::execute(){
                                numFastaSeqs = positions.size();
                                
                                int numSeqsPerProcessor = numFastaSeqs / processors;
-                               
+       
                                for (int i = 0; i < processors; i++) {
-                                       int startPos = positions[ i * numSeqsPerProcessor ];
+                                       unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
                                        if(i == processors - 1){
                                                numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
                                        }
@@ -761,9 +761,9 @@ int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFNa
 
                for(int i=0;i<line->numSeqs;i++){
                        if (m->control_pressed) { return 0; }
-                       
-                       Sequence* candidateSeq = new Sequence(inFASTA);
-                       
+               
+                       Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+               
                        if (candidateSeq->getName() != "") {
                                taxonomy = classify->getTaxonomy(candidateSeq);