X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=36cc7766f03097235fa274f12330611d616cdacb;hb=fb01d5df390a98313ca095a812fc240dc079d084;hp=f2dfdd5bae38d5994ff03150013aab9db0ecfb7c;hpb=67b6343929b6dbed97c4b26c3bb849725d573f6d;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index f2dfdd5..36cc776 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -17,8 +17,11 @@ int DeconvoluteCommand::execute() {
 		//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();
@@ -29,7 +32,8 @@ int DeconvoluteCommand::execute() {
 		//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;
 	}