X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=6041c95d59952fbaf1c856055181d4e145c3a9c0;hb=HEAD;hp=b17d9ed6799d9c8287664cf63241b0fde01bf40e;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index b17d9ed..6041c95 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -558,7 +558,7 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
 
 			}
 			
-			if((i+1) % 100 == 0){	cout << (i+1) << endl;	 m->mothurOutJustToLog(toString(i+1) + "\n");	}
+			if((i+1) % 100 == 0){	cout << (i+1) << endl;		}
 		}
 		
 		if(outputString != ""){ //output to file 
@@ -572,7 +572,7 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
 			delete buf;
 		}
 		
-		if((num) % 100 != 0){	cout << (num) << endl;	 m->mothurOutJustToLog(toString(num) + "\n");	}
+		if((num) % 100 != 0){	cout << (num) << endl;	 	}
 			
 		return 0;
 	}
@@ -623,10 +623,10 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+			if((count) % 100 == 0){	m->mothurOutJustToScreen(toString(count)+"\n"); 	}
 		}
 		//report progress
-		if((count) % 100 != 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+		if((count) % 100 != 0){	m->mothurOutJustToScreen(toString(count)+"\n"); 		}
 		
 		
 		out.close();
@@ -653,18 +653,18 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, strin
 		
 		//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){
-				string filteredFasta = filename + toString(getpid()) + ".temp";
+				string filteredFasta = filename + m->mothurGetpid(process) + ".temp";
 				num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 				
 				//pass numSeqs to parent
 				ofstream out;
-				string tempFile = filename +  toString(getpid()) + ".num.temp";
+				string tempFile = filename +  m->mothurGetpid(process) + ".num.temp";
 				m->openOutputFile(tempFile, out);
 				out << num << endl;
 				out.close();
@@ -990,7 +990,8 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
 					
 			Sequence seq(in); m->gobble(in);
 			if (seq.getName() != "") {
-					if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
+                    if (m->debug) { m->mothurOut("[DEBUG]: " + seq.getName() + " length = " + toString(seq.getAligned().length())); m->mothurOutEndLine();}
+					if (seq.getAligned().length() != alignmentLength) { m->mothurOut("[ERROR]: Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 					
 					if(trump != '*')			{	F.doTrump(seq);		}
 					if(m->isTrue(vertical) || soft != 0)	{	F.getFreqs(seq);	}
@@ -1006,10 +1007,10 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+			if((count) % 100 == 0){	m->mothurOutJustToScreen(toString(count)+"\n"); 		}
 		}
 		//report progress
-		if((count) % 100 != 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+		if((count) % 100 != 0){	m->mothurOutJustToScreen(toString(count)+"\n"); 	}
 		in.close();
 		
 		return count;
@@ -1052,11 +1053,11 @@ int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File&
 			cout.flush();
 						
 			//report progress
-			if((i+1) % 100 == 0){	cout << (i+1) << endl;	 m->mothurOutJustToLog(toString(i+1) + "\n");	}
+			if((i+1) % 100 == 0){	cout << (i+1) << endl;		}
 		}
 		
 		//report progress
-		if((num) % 100 != 0){	cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n"); 	}
+		if((num) % 100 != 0){	cout << num << endl; 	}
 		
 		return 0;
 	}
@@ -1078,7 +1079,7 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, 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
@@ -1094,7 +1095,7 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
 				num = driverCreateFilter(F, filename, lines[process]);
 				
 				//write out filter counts to file
-				filename += toString(getpid()) + "filterValues.temp";
+				filename += m->mothurGetpid(process) + "filterValues.temp";
 				ofstream out;
 				m->openOutputFile(filename, out);