changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 5d8d6c4a87223dd1ec5573563f64b0b658cfcc1d..b6af15466c3f7fde3062760335c12e11025e7393 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -12,6 +12,7 @@
 
 
 #include "command.hpp"
+#include "sequence.hpp"
 
 class ChopSeqsCommand : public Command {
        
@@ -23,9 +24,12 @@ class ChopSeqsCommand : public Command {
                void help();    
                
        private:
-               string fastafile, outputDir;
+               string fastafile, outputDir, keep;
                bool abort;
-               int end;
+               int numbases;
+               
+               string getChopped(Sequence);
+               
 };
 
 #endif