fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 40dd09b9820b9689ab4d30ba9f5666ceb2e9573b..f267ba4b7859ed091f749456cb5495799ffc9ec0 100644 (file)
--- 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) {