X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=ac092083a53944207b926a6bb9d725a2249b571a;hb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;hp=18554399e43220b596723a745142b49d2d8c123e;hpb=8c616f2509abd2fb9485a38607c1b439d243b85c;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 1855439..ac09208 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -217,6 +217,7 @@ int ChimeraCheckCommand::execute(){
 
 			if (m->control_pressed) { delete chimera;	return 0;	}
 			
+			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
 			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
 			outputNames.push_back(outputFileName);
 			
@@ -269,8 +270,8 @@ int ChimeraCheckCommand::execute(){
 					
 					//wait on chidren
 					for(int j = 1; j < processors; j++) { 
-						char buf[4];
-						MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); 
+						char buf[5];
+						MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); 
 					}
 				}else{ //you are a child process
 					MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
@@ -288,9 +289,9 @@ int ChimeraCheckCommand::execute(){
 					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	}  delete chimera; return 0;  }
 					
 					//tell parent you are done.
-					char buf[4];
+					char buf[5];
 					strcpy(buf, "done"); 
-					MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
+					MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 				}
 				
 				//close files