fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 59c9b348ba1af9b719f35ae12a249265c7fe9662..2abe9ef78a8c76354d377087fa7a23deb27b4d25 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -194,12 +194,12 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                        }else { m->setAccnosFile(accnosfile); } 
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastafile == "not open") { abort = true; }
+                       if (fastafile == "not open") { fastafile = ""; abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
                        else { m->setFastaFile(fastafile); }
                                                                   
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
+                       if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
                        else { m->setNameFile(namefile); } 
                                                                   
@@ -237,6 +237,10 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                        
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, quality, alignreport or list."); m->mothurOutEndLine(); abort = true; }
                        
+                       if ((fastafile != "") && (namefile == "")) {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
                }
 
        }