linux screen.seqs segfault

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 6149ef5b7ded364733fa4480dc9386d2e7e92fb2..ee43bcbf72a2ca00af3e2270768f34ac1357bb71 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -70,7 +70,7 @@ private:
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
        #endif
 
-       bool abort, realign, trim, trimera, save, hasName, hasCount;
+       bool abort, realign, trim, trimera, save, hasName, hasCount, dups;
        string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
@@ -213,8 +213,6 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                        inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA); 
                }
                
-               pDataArray->count = pDataArray->end;
-               
                if (pDataArray->m->control_pressed) { out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera;  return 0;    }
                
                if (chimera->getUnaligned()) { 
@@ -227,7 +225,7 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                
                if (pDataArray->start == 0) { chimera->printHeader(out); }
                
-               int count = 0;
+               pDataArray->count = 0;
                for(int i = 0; i < pDataArray->end; i++){
                        
                        if (pDataArray->m->control_pressed) {   out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera; return 1;   }
@@ -318,18 +316,18 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                                        
                                        
                                }
-                               count++;
+                               pDataArray->count++;
                        }
                        
                        delete candidateSeq;
                        //report progress
-                       if((count) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine();         }
+                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }
                }
                //report progress
-               if((count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine();         }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }
                
                pDataArray->numNoParents = chimera->getNumNoParents();
-               if (pDataArray->numNoParents == count) {        pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }
+               if (pDataArray->numNoParents == pDataArray->count) {    pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }
 
                out.close();
                out2.close();