added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index ca029616870f97a31482a40497c645e240ae72db..9b02be9ef5ec0f5a50d0563ab87a7f7d053bdadc 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -34,7 +34,7 @@ private:
        bool compareDNASeq(string, string);
 
        bool abort;
-       string fastaFile, oligoFile, qFileName;
+       string fastaFile, oligoFile, qFileName, outputDir;
        
        bool flip, allFiles, qtrim;
        int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;