citation changes for 1.31.0

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 287f5a6acdc08a9c40b6e2e12b159a2f83fc9636..9538698a3fea181430056d11f16835f66186452e 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -45,7 +45,7 @@ string GetSeqsCommand::getHelpString(){
                helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, count, list, taxonomy, quality or alignreport file.\n";
                helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
                helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups.  You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";
-               helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n";
+               helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=true. \n";
                helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
                helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
                helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
@@ -587,7 +587,7 @@ int GetSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }