vector<string> setParameters();
string getCommandName() { return "trim.flows"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
string getDescription() { return "trim.flows"; }
flowData.printFlows(trimFlowFile);
- if(pDataArray->fasta) { currSeq.printSequence(fastaFile); }
+ if(pDataArray->fasta) { currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile); }
if(pDataArray->allFiles){
ofstream output;