added smart distance feature and optimized all commands using line by line processing

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index f2dfdd5bae38d5994ff03150013aab9db0ecfb7c..36cc7766f03097235fa274f12330611d616cdacb 100644 (file)
--- 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;
        }