summaryfile = validParameter.validFile(parameters, "summary", true);
if (summaryfile == "not open") { summaryfile = ""; abort = true; }
- else if (summaryfile == "not found") { summaryfile = ""; }
+ else if (summaryfile == "not found") { summaryfile = ""; }
+ else { m->setSummaryFile(summaryfile); }
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
it = badSeqNames.find(seqName);
if(it != badSeqNames.end()){
- badSeqNames.erase(it);
-
if(namefile != ""){
int start = 0;
for(int i=0;i<seqList.length();i++){
}
badSeqGroups[seqList.substr(start,seqList.length()-start)] = it->second;
}
+ badSeqNames.erase(it);
}
else{
goodNameOut << seqName << '\t' << seqList << endl;
saveName = name.substr(1);
while (!in.eof()) {
char c = in.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else { name += c; }
}
m->gobble(in);