X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=9538698a3fea181430056d11f16835f66186452e;hb=ace98dda2bb2e1cffd6755fb8a27e5080af66f2b;hp=480bde3222c9057aafecacc208d84eac24573b72;hpb=859e3a473a3e63e0060c49be70b80f9289253da2;p=mothur.git

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 480bde3..9538698 100644
--- 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";
@@ -501,7 +501,7 @@ int GetSeqsCommand::readQual(){
 				saveName = name.substr(1);
 				while (!in.eof())	{	
 					char c = in.get(); 
-					if (c == 10 || c == 13){	break;	}
+					if (c == 10 || c == 13 || c == -1){	break;	}
 					else { name += c; }	
 				} 
 				m->gobble(in);
@@ -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);
         }