added reverse.seqs command

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 05389072025dcaaf05b2dcaf5e3c4a3ab25c892b..3ad84795d784b5a633351021999159d01940ffdb 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -48,8 +48,8 @@ int ScreenSeqsCommand::execute(){
                
                set<string> badSeqNames;
                
-               string goodSeqFile = getRootName(globaldata->inputFileName) + "good" + getExtension(globaldata->inputFileName);
-               string badSeqFile = getRootName(globaldata->inputFileName) + "bad" + getExtension(globaldata->inputFileName);
+               string goodSeqFile = getRootName(globaldata->getFastaFile()) + "good" + getExtension(globaldata->getFastaFile());
+               string badSeqFile = getRootName(globaldata->getFastaFile()) + "bad" + getExtension(globaldata->getFastaFile());
                
                ofstream goodSeqOut;    openOutputFile(goodSeqFile, goodSeqOut);
                ofstream badSeqOut;             openOutputFile(badSeqFile, badSeqOut);          
@@ -73,6 +73,12 @@ int ScreenSeqsCommand::execute(){
                        }
                        gobble(inFASTA);
                }       
+               if(globaldata->getNameFile() != ""){
+                       screenNameGroupFile(badSeqNames);
+               }
+               else if(globaldata->getGroupFile() != ""){
+                       screenGroupFile(badSeqNames);
+               }
                
                return 0;
        }