distCalc = new eachGapDist();
decalc = new DeCalculator();
- mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
+ mapInfo = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "mapinfo";
#ifdef USE_MPI
- char inFileName[mapInfo.length()];
+ //char* inFileName = new char[mapInfo.length()];
+ //memcpy(inFileName, mapInfo.c_str(), mapInfo.length());
+
+ char inFileName[1024];
strcpy(inFileName, mapInfo.c_str());
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
MPI_File_open(MPI_COMM_WORLD, inFileName, outMode, MPI_INFO_NULL, &outMap); //comm, filename, mode, info, filepointer
+ //delete inFileName;
+
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_Status status;
int length = outString.length();
- char buf2[length];
- strcpy(buf2, outString.c_str());
+ char* buf2 = new char[length];
+ memcpy(buf2, outString.c_str(), length);
MPI_File_write_shared(outMap, buf2, length, MPI_CHAR, &status);
+ delete buf2;
}
#else
ofstream out2;
- openOutputFile(mapInfo, out2);
+ m->openOutputFile(mapInfo, out2);
out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
out2.close();
try {
ofstream out2;
- openOutputFileAppend(mapInfo, out2);
+ m->openOutputFileAppend(mapInfo, out2);
out2 << querySeq->getName() << endl;
for (it = spotMap.begin(); it!= spotMap.end(); it++) {
MPI_Status status;
int length = outString.length();
- char buf2[length];
- strcpy(buf2, outString.c_str());
+ char* buf2 = new char[length];
+ memcpy(buf2, outString.c_str(), length);
MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
-
+ delete buf2;
+
if (results) {
m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
outAccString += querySeq->getName() + "\n";
MPI_Status statusAcc;
length = outAccString.length();
- char buf[length];
- strcpy(buf, outAccString.c_str());
+ char* buf = new char[length];
+ memcpy(buf, outAccString.c_str(), length);
MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
+ delete buf;
}
//free memory
try {
MPI_Status status;
int length = output.length();
- char buf[length];
- strcpy(buf, output.c_str());
+ char* buf = new char[length];
+ memcpy(buf, output.c_str(), length);
MPI_File_write_shared(outMap, buf, length, MPI_CHAR, &status);
+ delete buf;
}
catch(exception& e) {