From: westcott <westcott>
Date: Wed, 1 Jun 2011 14:36:06 +0000 (+0000)
Subject: added count.seqs command and made some modifcations to the uchime code to allow it... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=75962c819c16814e5c2340d99af1aa62e564dc20

added count.seqs command and made some modifcations to the uchime code to allow it to build properly in cygwin
---

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 546a2f6..9699584 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -39,6 +39,7 @@
 		A74D369C137DAB8400332B0C /* writechhit.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3686137DAB8300332B0C /* writechhit.cpp */; };
 		A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */; };
 		A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; };
+		A7730EFF13967241007433A3 /* countseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7730EFE13967241007433A3 /* countseqscommand.cpp */; };
 		A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */; };
 		A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */; };
 		A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; };
@@ -401,6 +402,8 @@
 		A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerauchimecommand.cpp; sourceTree = "<group>"; };
 		A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = "<group>"; };
 		A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = "<group>"; };
+		A7730EFD13967241007433A3 /* countseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = countseqscommand.h; sourceTree = "<group>"; };
+		A7730EFE13967241007433A3 /* countseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countseqscommand.cpp; sourceTree = "<group>"; };
 		A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcommandinfocommand.h; sourceTree = "<group>"; };
 		A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcommandinfocommand.cpp; sourceTree = "<group>"; };
 		A77A221D139001B600B0BE70 /* deuniquetreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deuniquetreecommand.h; sourceTree = "<group>"; };
@@ -1221,6 +1224,8 @@
 				A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
 				A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */,
 				A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
+				A7730EFD13967241007433A3 /* countseqscommand.h */,
+				A7730EFE13967241007433A3 /* countseqscommand.cpp */,
 				A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */,
 				A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */,
 				A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */,
@@ -2101,6 +2106,7 @@
 				A74D369C137DAB8400332B0C /* writechhit.cpp in Sources */,
 				A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */,
 				A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */,
+				A7730EFF13967241007433A3 /* countseqscommand.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
diff --git a/blastdb.cpp b/blastdb.cpp
index c7003f4..48b09fb 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -35,9 +35,9 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		formatdbCommand = path + "blast/bin/formatdb";	//	format the database, -o option gives us the ability
 #else
-		formatdbCommand = path + "blast\\bin\\formatdb";
+		formatdbCommand = path + "blast\\bin\\formatdb.exe";
 		//wrap entire string in ""
-		formatdbCommand = "\"" + formatdbCommand + "\"";
+		//formatdbCommand = "\"" + formatdbCommand + "\"";
 #endif
 		
 		//test to make sure formatdb exists
@@ -50,9 +50,9 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		blastCommand = path + "blast/bin/blastall";	//	format the database, -o option gives us the ability
 #else
-		blastCommand = path + "blast\\bin\\blastall";
+		blastCommand = path + "blast\\bin\\blastall.exe";
 		//wrap entire string in ""
-		blastCommand = "\"" + blastCommand + "\"";
+		//blastCommand = "\"" + blastCommand + "\"";
 #endif
 		
 		//test to make sure formatdb exists
@@ -66,9 +66,9 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		megablastCommand = path + "blast/bin/megablast";	//	format the database, -o option gives us the ability
 #else
-		megablastCommand = path + "blast\\bin\\megablast";
+		megablastCommand = path + "blast\\bin\\megablast.exe";
 		//wrap entire string in ""
-		megablastCommand = "\"" + blastCommmegablastCommandand + "\"";
+		//megablastCommand = "\"" + megablastCommand + "\"";
 #endif
 		
 		//test to make sure formatdb exists
@@ -105,9 +105,9 @@ BlastDB::BlastDB() : Database() {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		formatdbCommand = path + "blast/bin/formatdb";	//	format the database, -o option gives us the ability
 #else
-		formatdbCommand = path + "blast\\bin\\formatdb";
+		formatdbCommand = path + "blast\\bin\\formatdb.exe";
 		//wrap entire string in ""
-		formatdbCommand = "\"" + formatdbCommand + "\"";
+		//formatdbCommand = "\"" + formatdbCommand + "\"";
 #endif
 		
 		//test to make sure formatdb exists
@@ -120,9 +120,9 @@ BlastDB::BlastDB() : Database() {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		blastCommand = path + "blast/bin/blastall";	//	format the database, -o option gives us the ability
 #else
-		blastCommand = path + "blast\\bin\\blastall";
+		blastCommand = path + "blast\\bin\\blastall.exe";
 		//wrap entire string in ""
-		blastCommand = "\"" + blastCommand + "\"";
+		//blastCommand = "\"" + blastCommand + "\"";
 #endif
 		
 		//test to make sure formatdb exists
@@ -136,9 +136,9 @@ BlastDB::BlastDB() : Database() {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		megablastCommand = path + "blast/bin/megablast";	//	format the database, -o option gives us the ability
 #else
-		megablastCommand = path + "blast\\bin\\megablast";
+		megablastCommand = path + "blast\\bin\\megablast.exe";
 		//wrap entire string in ""
-		megablastCommand = "\"" + blastCommmegablastCommandand + "\"";
+		//megablastCommand = "\"" + megablastCommand + "\"";
 #endif
 		
 		//test to make sure formatdb exists
diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index b00cedf..97b331b 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -1127,7 +1127,7 @@ vector<Sequence> ChimeraSlayer::getBlastSeqs(Sequence q, vector<Sequence*>& db,
 		delete queryRight;
 		delete queryLeft;
 		
-		if (refResults.size() == 0) { m->mothurOut("[WARNING]: megablast found 0 potential parents, so we are not able to check " + q.getName() + ". This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+		if (refResults.size() == 0) { m->mothurOut("[WARNING]: megablast returned 0 potential parents, so we are not able to check " + q.getName() + ". This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
 		
 		return refResults;
 	}
diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index d4cb57a..33b48bd 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -744,7 +744,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 		processIDS.clear();
 		int process = 1;
 		int num = 0;
-		
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)		
 		//break up file into multiple files
 		vector<string> files;
 		m->divideFile(filename, processors, files);
@@ -852,7 +852,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 #endif		
 		//get rid of the file pieces.
 		for (int i = 0; i < files.size(); i++) { remove(files[i].c_str()); }
-		
+#endif		
 		return num;	
 	}
 	catch(exception& e) {
diff --git a/commandfactory.cpp b/commandfactory.cpp
index 71558a9..620536d 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -119,6 +119,7 @@
 #include "sharedcommand.h"
 #include "getcommandinfocommand.h"
 #include "deuniquetreecommand.h"
+#include "countseqscommand.h"
 
 /*******************************************************/
 
@@ -241,6 +242,7 @@ CommandFactory::CommandFactory(){
 	commands["set.current"]			= "set.current";
 	commands["get.commandinfo"]		= "get.commandinfo";
 	commands["deunique.tree"]		= "deunique.tree";
+	commands["count.seqs"]			= "count.seqs";
 	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
@@ -412,6 +414,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "make.shared")			{	command = new SharedCommand(optionString);					}
 		else if(commandName == "get.commandinfo")		{	command = new GetCommandInfoCommand(optionString);			}
 		else if(commandName == "deunique.tree")			{	command = new DeuniqueTreeCommand(optionString);			}
+		else if(commandName == "count.seqs")			{	command = new CountSeqsCommand(optionString);				}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -549,6 +552,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "make.shared")			{	pipecommand = new SharedCommand(optionString);					}
 		else if(commandName == "get.commandinfo")		{	pipecommand = new GetCommandInfoCommand(optionString);			}
 		else if(commandName == "deunique.tree")			{	pipecommand = new DeuniqueTreeCommand(optionString);			}
+		else if(commandName == "count.seqs")			{	pipecommand = new CountSeqsCommand(optionString);				}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -674,6 +678,7 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "make.shared")			{	shellcommand = new SharedCommand();					}
 		else if(commandName == "get.commandinfo")		{	shellcommand = new GetCommandInfoCommand();			}
 		else if(commandName == "deunique.tree")			{	shellcommand = new DeuniqueTreeCommand();			}
+		else if(commandName == "count.seqs")			{	shellcommand = new CountSeqsCommand();				}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;
diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 8164e27..a446469 100644
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -33,7 +33,7 @@ vector<string> CountSeqsCommand::setParameters(){
 string CountSeqsCommand::getHelpString(){	
 	try {
 		string helpString = "";
-		helpString += "The count.seqs command reads a name file and outputs a .count.summary file.  You may also provide a group file to get the counts broken down by group.\n";
+		helpString += "The count.seqs command reads a name file and outputs a .seq.count file.  You may also provide a group file to get the counts broken down by group.\n";
 		helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
 		helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
 		helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
@@ -146,7 +146,7 @@ int CountSeqsCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		ofstream out;
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "count.summary";
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + ".seq.count";
 		m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
 		out << "Representative Sequence\t total\t";
 		
diff --git a/countseqscommand.h b/countseqscommand.h
new file mode 100644
index 0000000..385cd13
--- /dev/null
+++ b/countseqscommand.h
@@ -0,0 +1,41 @@
+#ifndef COuNTSEQSCOMMAND_H
+#define COuNTSEQSCOMMAND_H
+
+/*
+ *  countseqscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 6/1/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+class CountSeqsCommand : public Command {
+	
+public:
+	
+	CountSeqsCommand(string);
+	CountSeqsCommand();	
+	~CountSeqsCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "count.seqs";				}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+	
+private:
+	string namefile, groupfile, outputDir, groups;
+	bool abort;
+	vector<string> Groups;
+};
+
+#endif
+
+
diff --git a/myutils.cpp b/myutils.cpp
index e9d52c2..b9c0147 100755
--- a/myutils.cpp
+++ b/myutils.cpp
@@ -13,19 +13,19 @@
 #include <signal.h>
 #include <float.h>
 
-#ifdef _MSC_VER
-#include <crtdbg.h>
-#include <process.h>
-#include <windows.h>
-#include <psapi.h>
-#include <io.h>
-#else
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 #include <sys/time.h>
 #include <sys/resource.h>
 #include <unistd.h>
 #include <errno.h>
 #include <fcntl.h>
 #include <stdlib.h>
+#else
+//#include <crtdbg.h>
+#include <process.h>
+#include <windows.h>
+#include <psapi.h>
+#include <io.h>
 #endif
 
 #include "myutils.h"
@@ -141,7 +141,9 @@ bool myisatty(int fd)
 	return isatty(fd) != 0;
 	}
 
-#ifdef _MSC_VER
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+#ifdef BIT_VERSION
 #include <io.h>
 int fseeko(FILE *stream, off_t offset, int whence)
 	{
@@ -149,6 +151,14 @@ int fseeko(FILE *stream, off_t offset, int whence)
 	return (FilePos == -1L) ? -1 : 0;
 	}
 #define ftello(fm) (off_t) _ftelli64(fm)
+#else 
+int fseeko(FILE *stream, off_t offset, int whence)
+{
+	off_t FilePos = fseek(stream, offset, whence);
+	return (FilePos == -1L) ? -1 : 0;
+}
+#define ftello(fm) (off_t) ftell(fm)
+#endif
 #endif
 
 void LogStdioFileState(FILE *f)
@@ -168,9 +178,16 @@ void LogStdioFileState(FILE *f)
 	Log("fpos       %ld (retval %d)\n", (long) fpos, fgetpos_retval);
 //	Log("eof        %d\n", _eof(fd));
 #endif
-#ifdef _MSC_VER
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+#ifdef BIT_VERSION
 	__int64 pos64 = _ftelli64(f);
 	Log("_ftelli64  %lld\n", pos64);
+#else
+	__int32 pos32 = ftell(f);
+	Log("ftell  %lld\n", pos32);
+		
+#endif
 #endif
 	}
 
@@ -596,10 +613,11 @@ void Die(const char *Format, ...)
 	fprintf(stderr, "\n---Fatal error---\n%s\n", szStr);
 	Log("\n---Fatal error---\n%s\n", szStr);
 
-#ifdef _MSC_VER
-	if (IsDebuggerPresent())
- 		__debugbreak();
-	_CrtSetDbgFlag(0);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+	//if (IsDebuggerPresent())
+ 	//	__debugbreak();
+	//_CrtSetDbgFlag(0);
 #endif
 
 	exit(1);
@@ -624,20 +642,7 @@ void Warning(const char *Format, ...)
 		}
 	}
 
-#ifdef _MSC_VER
-double GetMemUseBytes()
-	{
-	HANDLE hProc = GetCurrentProcess();
-	PROCESS_MEMORY_COUNTERS PMC;
-	BOOL bOk = GetProcessMemoryInfo(hProc, &PMC, sizeof(PMC));
-	if (!bOk)
-		return 1000000;
-	double Bytes = (double) PMC.WorkingSetSize;
-	if (Bytes > g_PeakMemUseBytes)
-		g_PeakMemUseBytes = Bytes;
-	return Bytes;
-	}
-#elif	linux || __linux__
+#if defined linux || __linux__
 double GetMemUseBytes()
 	{
 	static char statm[64];
@@ -668,7 +673,7 @@ double GetMemUseBytes()
 		g_PeakMemUseBytes = Bytes;
 	return Bytes;
 	}
-#elif defined(__MACH__)
+#elif defined(__APPLE__) || (__MACH__)
 #include <memory.h>
 #include <stdlib.h>
 #include <stdio.h>
@@ -709,9 +714,9 @@ double GetMemUseBytes()
 	}
 #else
 double GetMemUseBytes()
-	{
+{
 	return 0;
-	}
+}
 #endif
 
 double GetPeakMemUseBytes()
@@ -1201,7 +1206,8 @@ static void AddOpt(const OptInfo &Opt)
 	g_Opts.insert(Opt);
 	}
 
-#ifdef _MSC_VER
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
 #pragma warning(disable: 4505) // unreferenced local function
 #endif
 
diff --git a/myutils.h b/myutils.h
index 6122054..6374c8b 100644
--- a/myutils.h
+++ b/myutils.h
@@ -16,30 +16,32 @@
 #include <cstdlib>
 #include <climits>
 
-#ifndef _MSC_VER
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
 #include <inttypes.h>
 #endif
 
 using namespace std;
 
-#ifdef _MSC_VER
-#include <crtdbg.h>
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+//#include <crtdbg.h>
 #pragma warning(disable: 4996)	// deprecated functions
 #define _CRT_SECURE_NO_DEPRECATE	1
 #endif
 
-#if defined(_DEBUG) && !defined(DEBUG)
+//#if defined(_DEBUG) && !defined(DEBUG)
 #define DEBUG	1
-#endif
+//#endif
 
-#if defined(DEBUG) && !defined(_DEBUG)
+//#if defined(DEBUG) && !defined(_DEBUG)
 #define _DEBUG	1
-#endif
+//#endif
 
-#ifndef NDEBUG
+//#ifndef NDEBUG
 #define	DEBUG	1
 #define	_DEBUG	1
-#endif
+//#endif
 
 typedef unsigned char byte;
 typedef unsigned short uint16;
@@ -49,10 +51,10 @@ typedef double float32;
 typedef signed char int8;
 typedef unsigned char uint8;
 
-#ifdef _MSC_VER
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 
-typedef __int64 int64;
-typedef unsigned __int64 uint64;
+typedef long long int64;
+typedef unsigned long long uint64;
 
 #define INT64_PRINTF		"lld"
 #define UINT64_PRINTF		"llu"
@@ -66,6 +68,7 @@ typedef unsigned __int64 uint64;
 #define SIZE_T_PRINTFX		"x"
 #define OFF64_T_PRINTFX		"llx"
 
+
 #elif defined(__x86_64__)
 
 typedef long int64;
@@ -85,8 +88,8 @@ typedef unsigned long uint64;
 
 #else
 
-typedef long long int64;
-typedef unsigned long long uint64;
+typedef __int64 int64;
+typedef unsigned __int64 uint64;
 
 #define INT64_PRINTF		"lld"
 #define UINT64_PRINTF		"llu"
@@ -99,6 +102,7 @@ typedef unsigned long long uint64;
 
 #define SIZE_T_PRINTFX		"x"
 #define OFF64_T_PRINTFX		"llx"
+
 #endif
 
 #define d64		INT64_PRINTF
@@ -160,7 +164,8 @@ void myfree(void *p);
 
 bool myisatty(int fd);
 
-#ifdef _MSC_VER
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
 #define off_t	__int64
 #endif
 
diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 2774922..5efb1ce 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -347,6 +347,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
 		processIDS.clear();
 		map<char, vector<int> >::iterator it;
 		int num = 0;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
@@ -569,7 +570,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
 			in.close(); remove(tempFile.c_str());
 			
 		}
-		
+#endif		
 		return num;
 	}
 	catch(exception& e) {
diff --git a/systemcommand.cpp b/systemcommand.cpp
index e5aeb3e..5ace75e 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -91,20 +91,23 @@ int SystemCommand::execute(){
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		//system(command.c_str());
-		FILE *lsofFile_p = popen(command.c_str(), "r");
+		command += " > ./commandScreen.output 2>&1";
+		system(command.c_str());
 		
-		if (!lsofFile_p) { return 0; }
+		ifstream in;
+		string filename = "./commandScreen.output";
+		m->openInputFile(filename, in);
 		
-		char buffer[1024];
-		while ( fgets(buffer, 1024, lsofFile_p) != NULL ) {
-			string temp = buffer;
-			m->mothurOut(temp); 
+		string output = "";
+		while(char c = in.get()){
+			if(in.eof())		{	break;			}
+			else				{	output += c;	}
 		}
-		m->mothurOutEndLine();
-		
-		pclose(lsofFile_p);
+		in.close();
 		
+		m->mothurOut(output); m->mothurOutEndLine();
+		remove(filename.c_str());
+				
 		return 0;		
 	}
 
diff --git a/timing.h b/timing.h
index 10bd1f7..4db7847 100644
--- a/timing.h
+++ b/timing.h
@@ -59,30 +59,29 @@ const unsigned AllocerCount =
 #undef A
 	;
 
-#ifdef _MSC_VER
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+typedef uint64_t TICKS;
+__inline__ uint64_t GetClockTicks()
+{
+	uint32_t lo, hi;
+	/* We cannot use "=A", since this would use %rax on x86_64 */
+	__asm__ __volatile__ ("rdtsc" : "=a" (lo), "=d" (hi));
+	return (uint64_t)hi << 32 | lo;
+}
 
+
+#else	// ifdef _MSC_VER
 typedef unsigned __int64 TICKS;
 
 #pragma warning(disable:4035)
 inline TICKS GetClockTicks()
-	{
+{
 	_asm
-		{
+	{
 		_emit	0x0f
 		_emit	0x31
-		}
-	}
-
-#else	// ifdef _MSC_VER
-
-typedef uint64_t TICKS;
-__inline__ uint64_t GetClockTicks()
-	{
-	uint32_t lo, hi;
-	/* We cannot use "=A", since this would use %rax on x86_64 */
-	__asm__ __volatile__ ("rdtsc" : "=a" (lo), "=d" (hi));
-	return (uint64_t)hi << 32 | lo;
 	}
+}
 
 #endif	// ifdef _MSC_VER