fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 400a715aeedf604efb80e580f6c345677f74a430..cc486d3ab690fd655c1de8a22ae406eafc2c242f 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -281,7 +281,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 
                        string 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, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -306,14 +306,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                        
                        
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
-                       convert(temp, ksize);
+                       m->mothurConvert(temp, ksize);
                        
                        temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
                        svg = m->isTrue(temp);
                        if (nameFileNames.size() != 0) { svg = true; }
                        
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
-                       convert(temp, increment);                       
+                       m->mothurConvert(temp, increment);                      
                }
        }
        catch(exception& e) {
@@ -427,7 +427,7 @@ int ChimeraCheckCommand::execute(){
                        
                        
                        //break up file
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                vector<unsigned long long> positions = m->divideFile(fastaFileNames[i], processors);
                        
                                for (int s = 0; s < (positions.size()-1); s++) {
@@ -522,7 +522,7 @@ int ChimeraCheckCommand::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
@@ -599,7 +599,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 
 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 0;
                int num = 0;