removed make count from make.contigs

[mothur.git] / primerdesigncommand.cpp

diff --git a/primerdesigncommand.cpp b/primerdesigncommand.cpp
index f6ec7b591c5926070eb33e12022920347ace8107..59369b3cf7411bdc0383d2a0be0676c3caee4c61 100644 (file)
--- a/primerdesigncommand.cpp
+++ b/primerdesigncommand.cpp
@@ -39,7 +39,7 @@ vector<string> PrimerDesignCommand::setParameters(){
 string PrimerDesignCommand::getHelpString(){   
        try {
                string helpString = "";
-               helpString += "The primer.design allows you to design sequence fragments that are specific to particular OTUs.\n";
+               helpString += "The primer.design allows you to identify sequence fragments that are specific to particular OTUs.\n";
                helpString += "The primer.design command parameters are: list, fasta, name, count, otunumber, cutoff, length, pdiffs, mintm, maxtm, processors and label.\n";
                helpString += "The list parameter allows you to provide a list file and is required.\n";
         helpString += "The fasta parameter allows you to provide a fasta file and is required.\n";
@@ -889,7 +889,9 @@ vector<Sequence> PrimerDesignCommand::createProcessesConSeqs(map<string, int>& n
         
         
 #else
-               counts = driverGetCounts(nameMap, fastaCount, otuCounts, 0, 1000);      
+        unsigned long long start = 0;
+        unsigned long long end = 1000;
+               counts = driverGetCounts(nameMap, fastaCount, otuCounts, start, end);   
 #endif         
         
         //you will have a nameMap error if there is a namefile or countfile, but if those aren't given we want to make sure the fasta and list file match.