X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=64ed9faa73e7cb72e5e307cc10e86f1a9bcfc195;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=6caa606dc10ee387cd2eb829d264a7d17f0ee670;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 6caa606..64ed9fa 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -38,7 +38,7 @@ string ChimeraCheckCommand::getHelpString(){
 	try {
 		string helpString = "";
 		helpString += "The chimera.check command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
-		helpString += "This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
+		helpString += "This command was created using the algorithms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
 		helpString += "The chimera.check command parameters are fasta, reference, processors, ksize, increment, svg and name.\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";
@@ -547,11 +547,10 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
-            count++;
+			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();
 		inFASTA.close();
@@ -599,10 +598,10 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 			delete candidateSeq;
 			
 			//report progress
-			if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;	m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");		}
+			if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;		}
 		}
 		//report progress
-		if(num % 100 != 0){		cout << "Processing sequence: " << num << endl;	m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); 	}
+		if(num % 100 != 0){		cout << "Processing sequence: " << num << endl;		}
 		
 		return 0;
 	}