X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraccodecommand.cpp;h=d890db4087813cc3c4c4e453b55013fa555e7689;hp=7adf82814ee5447edef7e203bbb046ad61c51b07;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 7adf828..d890db4 100644
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -38,7 +38,7 @@ string ChimeraCcodeCommand::getHelpString(){
 	try {
 		string helpString = "";
 		helpString += "The chimera.ccode command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
-		helpString += "This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n";
+		helpString += "This command was created using the algorithms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n";
 		helpString += "The chimera.ccode command parameters are fasta, reference, filter, mask, processors, window and numwanted.\n";
 		helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required unless you have a valid current fasta file. \n";
 		helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
@@ -548,10 +548,10 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+			if((count) % 100 == 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");		}
 		}
 		//report progress
-		if((count) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+		if((count) % 100 != 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");	}
 		
 		out.close();
 		out2.close();