X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.cpp;h=f267ba4b7859ed091f749456cb5495799ffc9ec0;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=40dd09b9820b9689ab4d30ba9f5666ceb2e9573b;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;p=mothur.git

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 40dd09b..f267ba4 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -306,6 +306,7 @@ int SffInfoCommand::execute(){
 			
 			int start = time(NULL);
 			
+            filenames[s] = m->getFullPathName(filenames[s]);
 			m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 			
 			string accnos = "";
@@ -361,6 +362,9 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
 
 		ofstream outSfftxt, outFasta, outQual, outFlow;
 		string outFastaFileName, outQualFileName;
+        string rootName = outputDir + m->getRootName(m->getSimpleName(input));
+        if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
+        
 		string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
 		string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
 		if (trim) {