X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=primerdesigncommand.cpp;h=195adf4f716b29bd7c12a2f3529603e4baec6b4d;hp=f6ec7b591c5926070eb33e12022920347ace8107;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=4b54ce99af7db8019ea907cd7c2edf789369ada9

diff --git a/primerdesigncommand.cpp b/primerdesigncommand.cpp
index f6ec7b5..195adf4 100644
--- 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.
@@ -1086,7 +1088,7 @@ map<string, int> PrimerDesignCommand::readCount(unsigned long int& numSeqs){
         map<string, int> nameMap;
         
         CountTable ct;
-        ct.readTable(countfile);
+        ct.readTable(countfile, false);
         vector<string> namesOfSeqs = ct.getNamesOfSeqs();
         numSeqs = ct.getNumUniqueSeqs();