kmerSize = k;
outputDir = o;
- templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0);
+ templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0, rand());
m->mothurOutEndLine();
kmer = new Kmer(kmerSize);
}
}
//***************************************************************************************************************
-int ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
+Sequence ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
try {
m->mothurOut("Processing: " + querySeq->getName()); m->mothurOutEndLine();
}
}
- return 0;
+ return *querySeq;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "print");
}
#ifdef USE_MPI
//***************************************************************************************************************
-int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
+Sequence ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
try {
cout << "Processing: " << querySeq->getName() << endl;
}
}
- return 0;
+ return *querySeq;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "print");
delete buffer;
while(!iss.eof()) {
- iss >> name; gobble(iss);
+ iss >> name; m->gobble(iss);
names[name] = name;
}
#else
ifstream in;
- openInputFile(namefile, in);
+ m->openInputFile(namefile, in);
while (!in.eof()) {
- in >> name; gobble(in);
+ in >> name; m->gobble(in);
names[name] = name;
}
in.close();
try{
int common = 0;
- map<int, int>::iterator small;
- map<int, int>::iterator large;
+ map<int, int>::iterator smallone;
+ map<int, int>::iterator largeone;
+
if (query.size() < subject.size()) {
- for (small = query.begin(); small != query.end(); small++) {
- large = subject.find(small->first);
+ for (smallone = query.begin(); smallone != query.end(); smallone++) {
+ largeone = subject.find(smallone->first);
//if you found it they have that kmer in common
- if (large != subject.end()) { common++; }
+ if (largeone != subject.end()) { common++; }
}
}else {
- for (small = subject.begin(); small != subject.end(); small++) {
- large = query.find(small->first);
+ for (smallone = subject.begin(); smallone != subject.end(); smallone++) {
+ largeone = query.find(smallone->first);
//if you found it they have that kmer in common
- if (large != query.end()) { common++; }
+ if (largeone != query.end()) { common++; }
}
}
string file = outputDir + querySeq->getName() + ".chimeracheck.svg";
ofstream outsvg;
- openOutputFile(file, outsvg);
+ m->openOutputFile(file, outsvg);
int width = (info.size()*5) + 150;