//trims seqs to first non gap char in all seqs and last non gap char in all seqs
spotMap = decalc->trimSeqs(query, refSeqs);
+
+ //you trimmed the whole sequence, skip
+ if (query->getAligned() == "") { return "no"; }
vector<Sequence*> temp = refSeqs;
temp.push_back(query);
//if coverage above minimum
if (coverage > minCoverage) {
newRefs.push_back(ref[i]);
+ }else {
+ delete ref[i];
}
}
return refResults;
}
catch(exception& e) {
- m->errorOut(e, "Maligner", "getBlastSeqs");
+ m->errorOut(e, "Maligner", "getKmerSeqs");
exit(1);
}
}