forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index f238094c9563587be29064a8f3fdbce54314c0f9..e28775f016c4e992d2d8f2d23904c93c6e3f74ef 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -12,7 +12,7 @@
 //#include "uc.h"
 #include "sequence.hpp"
 #include "referencedb.h"
-
+#include "systemcommand.h"
 
 //**********************************************************************************************************************
 vector<string> ChimeraUchimeCommand::setParameters(){  
@@ -463,10 +463,20 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                        string uchimeCommand;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        uchimeCommand = path + "uchime";        //      format the database, -o option gives us the ability
+            if (m->debug) { 
+                m->mothurOut("[DEBUG]: Uchime location using \"which uchime\" = "); 
+                Command* newCommand = new SystemCommand("which uchime"); m->mothurOutEndLine();
+                newCommand->execute();
+                delete newCommand;
+                m->mothurOut("[DEBUG]: Mothur's location using \"which mothur\" = "); 
+                newCommand = new SystemCommand("which mothur"); m->mothurOutEndLine();
+                newCommand->execute();
+                delete newCommand;
+            }
 #else
                        uchimeCommand = path + "uchime.exe";
 #endif
-                       
+        
                        //test to make sure uchime exists
                        ifstream in;
                        uchimeCommand = m->getFullPathName(uchimeCommand);
@@ -544,7 +554,7 @@ int ChimeraUchimeCommand::execute(){
                                int totalSeqs = 0;
                                
                                if(processors == 1)     {       totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups);     }
-                               else                            {       totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups);                      }
+                               else                            {       totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups, nameFile, groupFile, fastaFileNames[s]);                      }
 
                                if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        }  return 0;    }                               
 
@@ -1473,7 +1483,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 }
 /**************************************************************************************************/
 
-int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector<string> groups) {
+int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector<string> groups, string nameFile, string groupFile, string fastaFile) {
        try {
                
                processIDS.clear();
@@ -1552,7 +1562,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o
                        // Allocate memory for thread data.
                        string extension = toString(i) + ".temp";
                        
-                       uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastafile, namefile, groupfile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end,  i);
+                       uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastaFile, nameFile, groupFile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end,  i);
                        tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
                        tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);