X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.cpp;h=7fd2803a4ec6c5e578d7b180a9e08fda1af33385;hb=264c8a3c759d9a999c485236e98dac98d4f0db5f;hp=5df61889747833ef27f5929d227c849ea7245769;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;p=mothur.git

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 5df6188..7fd2803 100644
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -219,6 +219,13 @@ int DegapSeqsCommand::execute(){
 			if (m->control_pressed) {  outputTypes.clear(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} return 0; }
 		}
 		
+		//set fasta file as new current fastafile
+		string current = "";
+		itTypes = outputTypes.find("fasta");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+		}
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}