From 17fe3208075e55133789b247c062e6474f7439b0 Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Tue, 13 Mar 2012 15:43:41 -0400
Subject: [PATCH] fixed makefile

---
 makefile          |  8 ++++----
 shhhercommand.cpp | 30 ++++++++++++++++++++++++++++++
 2 files changed, 34 insertions(+), 4 deletions(-)

diff --git a/makefile b/makefile
index c389a94..100df10 100644
--- 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 28e6615..78bd73b 100644
--- 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{		
-- 
2.39.2