}
#endif
- if (ableToOpen == 1) { m->mothurOut("Unable to match group file with fasta file."); m->mothurOutEndLine(); abort = true; }
+ if (ableToOpen == 1) { m->mothurOut("Unable to match group file with fasta file, not using " + groupfileNames[i] + "."); m->mothurOutEndLine(); groupfileNames[i] = ""; }
}
}
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
start = time(NULL);
- PhyloSummary taxaSum(taxonomyFileName, groupfileNames[s]);
+ string group = "";
+ if (groupfile != "") { group = groupfileNames[s]; }
+
+ PhyloSummary taxaSum(taxonomyFileName, group);
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
}
//***************************************************************************************************************
-bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
+int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
try {
string rawSequence = seq.getUnaligned();
bool success = bdiffs + 1; //guilty until proven innocent
//***************************************************************************************************************
-bool TrimSeqsCommand::stripForward(Sequence& seq){
+int TrimSeqsCommand::stripForward(Sequence& seq){
try {
string rawSequence = seq.getUnaligned();
bool success = pdiffs + 1; //guilty until proven innocent
void getOligos(vector<string>&);
bool stripQualThreshold(Sequence&, ifstream&);
bool cullQualAverage(Sequence&, ifstream&);
- bool stripBarcode(Sequence&, int&);
- bool stripForward(Sequence&);
+ int stripBarcode(Sequence&, int&);
+ int stripForward(Sequence&);
bool stripReverse(Sequence&);
bool cullLength(Sequence&);
bool cullHomoP(Sequence&);