minor bugs fixes and added line and label options to read.otu's parselist and shared...

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index f2dfdd5bae38d5994ff03150013aab9db0ecfb7c..966fee03f90bf4fb87d39efdedf0189cc18f10be 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) + "uni_fasta");
+               
                openInputFile(filename, in);
                openOutputFile(outputFileName, out);
+               openOutputFile(outFastafile, outFasta);
        
                //constructor reads in file and store internally
                fastamap = new FastaMap();
@@ -30,6 +33,7 @@ int DeconvoluteCommand::execute() {
                //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->printCondensedFasta(outFasta);
        
                return 0;
        }