fixed makefile

diff --git a/makefile b/makefile
index c389a9468706d4ea214c7f4e3dfffc3c220da365..100df10d1ff4cfa8330ad226a8ea5a57b6f6777a 100644 (file)
--- a/makefile
+++ b/makefile
@@ -9,15 +9,15 @@
 # Macros
 #
 
-USEMPI ?= yes
+USEMPI ?= no
 64BIT_VERSION ?= yes
 USEREADLINE ?= no
 CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"3/12/2012\""
-VERSION = "\"1.24.4\""
-FORTAN_COMPILER = /usr/local/gfortran/bin/gfortran
+RELEASE_DATE = "\"3/13/2012\""
+VERSION = "\"1.24.0\""
+FORTAN_COMPILER = gfortran
 
 # Optimize to level 3:
 CXXFLAGS += -O3 

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 28e6615f3dffba8fb88c88cd9ca76e79e66faa06..78bd73b45bfa6e5bc1337eb81cd783d9a6f1ec82 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -719,6 +719,36 @@ int ShhherCommand::execute(){
        }
 }
 /**************************************************************************************************/
+string ShhherCommand::createNamesFile(){
+       try{
+               
+               vector<string> duplicateNames(numUniques, "");
+               for(int i=0;i<numSeqs;i++){
+                       duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
+               }
+               
+               string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+               
+               ofstream nameFile;
+               m->openOutputFile(nameFileName, nameFile);
+               
+               for(int i=0;i<numUniques;i++){
+                       
+                       if (m->control_pressed) { break; }
+                       
+            //                 nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
+                       nameFile << mapUniqueToSeq[i] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
+               }
+               
+               nameFile.close();
+               return  nameFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ShhherCommand", "createNamesFile");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
 
 string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
        try{