X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;h=b266025f1720d5c0ef7366d1ee7d155182f3fa21;hb=a89c6295ae9a35fcaaab7fa50dcb68360dd543b0;hp=7adf82814ee5447edef7e203bbb046ad61c51b07;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;p=mothur.git

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 7adf828..b266025 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();
@@ -633,17 +633,17 @@ int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename,
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
-			int pid = fork();
+			pid_t pid = fork();
 			
 			if (pid > 0) {
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
-				num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
+				num = driver(lines[process], outputFileName + toString(m->mothurGetpid(process)) + ".temp", filename, accnos + toString(m->mothurGetpid(process)) + ".temp");
 				
 				//pass numSeqs to parent
 				ofstream out;
-				string tempFile = outputFileName + toString(getpid()) + ".num.temp";
+				string tempFile = outputFileName + toString(m->mothurGetpid(process)) + ".num.temp";
 				m->openOutputFile(tempFile, out);
 				out << num << endl;
 				out.close();