MothurOut* m;
float match, misMatch, gapOpen, gapExtend;
int count, threshold, threadID, pdiffs, bdiffs, tdiffs;
- bool allFiles, createGroup;
+ bool allFiles, createGroup, done;
map<string, int> groupCounts;
map<string, string> groupMap;
vector<string> primerNameVector;
allFiles = all;
createGroup = cg;
threadID = tid;
+ done=false;
}
};
if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase); }
else if(pDataArray->align == "needleman") { alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, longestBase); }
- int num = 0;
+ pDataArray->count = 0;
string thisffastafile = pDataArray->files[0];
string thisfqualfile = pDataArray->files[1];
string thisrfastafile = pDataArray->files[2];
outScrapQual << endl;
}
}
- num++;
+ pDataArray->count++;
//report progress
- if((num) % 1000 == 0){ pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 1000 == 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
}
//report progress
- if((num) % 1000 != 0){ pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 1000 != 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
inFFasta.close();
inRFasta.close();
}
delete alignment;
+ pDataArray->done = true;
if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches); pDataArray->m->mothurRemove(pDataArray->outputScrapFasta); if (thisfqualfile != "") { pDataArray->m->mothurRemove(pDataArray->outputQual); pDataArray->m->mothurRemove(pDataArray->outputScrapQual); } }
return 0;