}
else{
if(reportFileName != ""){
- m->mothurOut("we are ignoring the report file if your sequences are not aligned. we will check that the sequences in your fasta and and qual fileare the same length.");
+ m->mothurOut("we are ignoring the report file if your sequences are not aligned. we will check that the sequences in your fasta and and qual file are the same length.");
m->mothurOutEndLine();
}
}
int numParentSeqs = -1;
int closestRefIndex = -1;
- numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned(), outChimeraReport);
+ string querySeq = query.getAligned();
+ if (!aligned) { querySeq = query.getUnaligned(); }
+
+ numParentSeqs = chimeraTest.analyzeQuery(query.getName(), querySeq, outChimeraReport);
closestRefIndex = chimeraTest.getClosestRefIndex();
string sname = ""; nameStream >> sname;
sname = sname.substr(1);
+
+ for (int i = 0; i < sname.length(); i++) {
+ if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+ }
map<string, int>::iterator it = firstSeqNames.find(sname);
istringstream nameStream(input);
string sname = ""; nameStream >> sname;
+ for (int i = 0; i < sname.length(); i++) {
+ if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+ }
+
map<string, int>::iterator it = firstSeqNamesReport.find(sname);
if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk