fixed some bugs and added mgcluster command

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 55f0b821b1392f40b1f6ecd2c9414a6f8a04fff2..96e1a7899c4fec8d769c46aede121bb8de240c07 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -209,22 +209,23 @@ int AlignCommand::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] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
                                }
                        }
                        inFASTA.close();
                        
                        numFastaSeqs = positions.size();
-                       
+               
                        int numSeqsPerProcessor = numFastaSeqs / processors;
                        
                        for (int i = 0; i < processors; i++) {
-                               int startPos = positions[ i * numSeqsPerProcessor ];
+                               long int startPos = positions[ i * numSeqsPerProcessor ];
                                if(i == processors - 1){
                                        numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
                                }
                                lines.push_back(new linePair(startPos, numSeqsPerProcessor));
                        }
+                       
                        createProcesses(alignFileName, reportFileName, accnosFileName); 
                        
                        rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
@@ -318,11 +319,11 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName,
 
                for(int i=0;i<line->numSeqs;i++){
                        
-                       Sequence* candidateSeq = new Sequence(inFASTA);
+                       Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
                        int origNumBases = candidateSeq->getNumBases();
                        string originalUnaligned = candidateSeq->getUnaligned();
                        int numBasesNeeded = origNumBases * threshold;
-                       
+       
                        if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
                                if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
                                        alignment->resize(candidateSeq->getUnaligned().length()+1);