distCalc = new eachGapDist();
decalc = new DeCalculator();
- mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
+ mapInfo = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "mapinfo";
#ifdef USE_MPI
#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++) {