//prepare filenames and open files
filename = globaldata->getFastaFile();
outputFileName = (getRootName(filename) + "names");
+ outFastafile = (getRootName(filename) + "unique.fasta");
+
openInputFile(filename, in);
openOutputFile(outputFileName, out);
+ openOutputFile(outFastafile, outFasta);
//constructor reads in file and store internally
fastamap = new FastaMap();
//print out new names file
//file contains 2 columns separated by tabs. the first column is the groupname(name of first sequence found.
//the second column is the list of names of identical sequences separated by ','.
- fastamap->print(out);
+ fastamap->printNamesFile(out);
+ fastamap->printCondensedFasta(outFasta);
return 0;
}