X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;h=fc98e0fc45c3b576a3e2420ac415c016266b4c1c;hb=8a0b2fd6644dee848b262fcdea73b912a6054fed;hp=7468011ee79e22c9f796733cb9db651f7e5e53f1;hpb=7f0cae4f4853cc3f12bc751ee06ea31c7c97496e;p=mothur.git diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp index 7468011..fc98e0f 100644 --- a/chimeraccodecommand.cpp +++ b/chimeraccodecommand.cpp @@ -223,13 +223,13 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; } - convert(temp, window); + m->mothurConvert(temp, window); temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "20"; } - convert(temp, numwanted); + m->mothurConvert(temp, numwanted); temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; } save = m->isTrue(temp); @@ -393,7 +393,7 @@ int ChimeraCcodeCommand::execute(){ //break up file - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) vector positions = m->divideFile(fastaFileNames[s], processors); for (int i = 0; i < (positions.size()-1); i++) { @@ -524,7 +524,7 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi } delete candidateSeq; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) unsigned long long pos = inFASTA.tellg(); if ((pos == -1) || (pos >= filePos->end)) { break; } #else @@ -611,7 +611,7 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) int process = 0; int num = 0;