refSeqs = getKmerSeqs(query, numWanted); //fills indexes
}else { m->mothurOut("not valid search."); exit(1); } //should never get here
refSeqs = getKmerSeqs(query, numWanted); //fills indexes
}else { m->mothurOut("not valid search."); exit(1); } //should never get here
fillScoreMatrix(matrix, refSeqs, chimeraPenalty);
vector<score_struct> path = extractHighestPath(matrix);
fillScoreMatrix(matrix, refSeqs, chimeraPenalty);
vector<score_struct> path = extractHighestPath(matrix);
vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
if (trace.size() > 1) { chimera = "yes"; }
vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
if (trace.size() > 1) { chimera = "yes"; }