MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//if you don't need to fork anything
if(processors == 1){
if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
/**************************************************************************************************/
void DistanceCommand::createProcesses(string filename) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 1;
processIDS.clear();
string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
//use the unix sort
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
string command = "sort -n " + outputFile + " -o " + outfile;
system(command.c_str());
#else //sort using windows sort
exit(1);
}
}
-/**************************************************************************************************
+**************************************************************************************************
int DistanceCommand::convertToLowerTriangle(string outputFile) {
try{
string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
//use the unix sort
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
string command = "sort -n " + outputFile + " -o " + outfile;
system(command.c_str());
#else //sort using windows sort
exit(1);
}
}
-/**************************************************************************************************/
+**************************************************************************************************/
//its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
//but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
//also check to make sure the 2 files have the same alignment length.