[med-svn] r9958 - trunk/packages/mothur/trunk/debian/patches
Andreas Tille
tille at alioth.debian.org
Thu Mar 8 14:41:02 UTC 2012
Author: tille
Date: 2012-03-08 14:41:01 +0000 (Thu, 08 Mar 2012)
New Revision: 9958
Modified:
trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch
trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch
trunk/packages/mothur/trunk/debian/patches/makefile.patch
trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch
Log:
Adapted patches to new upstream version
Modified: trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch 2012-03-08 14:38:55 UTC (rev 9957)
+++ trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch 2012-03-08 14:41:01 UTC (rev 9958)
@@ -2,8 +2,8 @@
Date: Thu, 10 Nov 2011 00:39:01 UTC
Closes: #648255
Description: Fix for FTBFS: cc1plus: error: unrecognized command line option '-msse2'
---- mothur-1.22.2.orig/uchime_src/mk
-+++ mothur-1.22.2/uchime_src/mk
+--- mothur-1.23.1.orig/uchime_src/mk
++++ mothur-1.23.1/uchime_src/mk
@@ -7,7 +7,7 @@
for CPPName in $CPPNames
do
Modified: trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch 2012-03-08 14:38:55 UTC (rev 9957)
+++ trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch 2012-03-08 14:41:01 UTC (rev 9958)
@@ -2,77 +2,279 @@
Date: Tue, 29 Nov 2011 22:50:55 +0100
Closes: #650683
Description: Enable build on BSD machines
---- mothur-1.22.2.orig/classifyseqscommand.h
-+++ mothur-1.22.2/classifyseqscommand.h
-@@ -128,7 +128,7 @@
+ Remark: This patch can be recreated by doing the following
+ cp -a mothur-<version> mothur-<version>.orig
+ cd mothur-<version>
+ sed -i 's/^\(#if defined.*\)(linux) || (__linux)\(.*\)$/\1(__unix__)\2/' *.h *.cpp
+ cd ..
+ diff -ubrN mothur-<version>.orig mothur-<version> > kfreebsd.patch
+ Andreas Tille <tille at debian.org>
+--- mothur-1.23.1.orig/aligncommand.cpp
++++ mothur-1.23.1/aligncommand.cpp
+@@ -826,7 +826,7 @@
+ try {
+ int num = 0;
+ processIDS.resize(0);
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+
+ //loop through and create all the processes you want
+--- mothur-1.23.1.orig/aligncommand.h
++++ mothur-1.23.1/aligncommand.h
+@@ -120,7 +120,7 @@
};
/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
#else
- static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
- classifyData* pDataArray;
---- mothur-1.22.2.orig/parsimony.cpp
-+++ mothur-1.22.2/parsimony.cpp
-@@ -54,7 +54,7 @@
- }
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
- }else{
-@@ -91,7 +91,7 @@
+ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
+ alignData* pDataArray;
+--- mothur-1.23.1.orig/bellerophon.cpp
++++ mothur-1.23.1/bellerophon.cpp
+@@ -356,7 +356,7 @@
- EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ int Bellerophon::createProcesses(vector<int> mid) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 1;
+ int process = 0;
+ int exitCommand = 1;
vector<int> processIDS;
+--- mothur-1.23.1.orig/blastdb.cpp
++++ mothur-1.23.1/blastdb.cpp
+@@ -24,7 +24,7 @@
+ int randNumber = rand();
+ //int randNumber = 12345;
+ string pid = "";
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ pid += getpid();
+ #else
+ pid += toString(threadID);
+@@ -42,7 +42,7 @@
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ path += "blast/bin/";
+ #else
+ path += "blast\\bin\\";
+@@ -51,7 +51,7 @@
---- mothur-1.22.2.orig/classifyseqscommand.cpp
-+++ mothur-1.22.2/classifyseqscommand.cpp
-@@ -383,7 +383,7 @@
- temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
- save = m->isTrue(temp);
- //this is so the threads can quickly load the reference data
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- #else
- if ((processors != 1) && (rdb->referenceSeqs.size() == 0)) { save = true; }
- #endif
-@@ -599,7 +599,7 @@
+
+ string formatdbCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
#else
+ formatdbCommand = path + "formatdb.exe";
+@@ -64,7 +64,7 @@
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
- vector<unsigned long long> positions;
+ string blastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- positions = m->divideFile(fastaFileNames[s], processors);
- for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
#else
-@@ -796,7 +796,7 @@
+ blastCommand = path + "blastall.exe";
+@@ -80,7 +80,7 @@
+
+
+ string megablastCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
+ #else
+ megablastCommand = path + "megablast.exe";
+@@ -114,7 +114,7 @@
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ path += "blast/bin/";
+ #else
+ path += "blast\\bin\\";
+@@ -123,7 +123,7 @@
+
+ int randNumber = rand();
+ string pid = "";
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ pid += getpid();
+ #else
+ pid += toString(threadID);
+@@ -134,7 +134,7 @@
+ blastFileName = pid + toString(randNumber) + ".blast";
+
+ string formatdbCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
+ #else
+ formatdbCommand = path + "formatdb.exe";
+@@ -149,7 +149,7 @@
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ string blastCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
+ #else
+ blastCommand = path + "blastall.exe";
+@@ -165,7 +165,7 @@
+
+
+ string megablastCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
+ #else
+ megablastCommand = path + "megablast.exe";
+--- mothur-1.23.1.orig/chimeraccodecommand.cpp
++++ mothur-1.23.1/chimeraccodecommand.cpp
+@@ -611,7 +611,7 @@
+
+ int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
int num = 0;
- processIDS.clear();
+--- mothur-1.23.1.orig/chimeracheckcommand.cpp
++++ mothur-1.23.1/chimeracheckcommand.cpp
+@@ -599,7 +599,7 @@
+
+ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
+ try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 1;
+ int process = 0;
+ int num = 0;
+--- mothur-1.23.1.orig/chimeraperseuscommand.cpp
++++ mothur-1.23.1/chimeraperseuscommand.cpp
+@@ -762,7 +762,7 @@
+ lines.push_back(linePair(startIndex, endIndex));
+ }
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+
//loop through and create all the processes you want
-@@ -965,7 +965,7 @@
- }
- delete candidateSeq;
+ while (process != processors) {
+--- mothur-1.23.1.orig/chimeraperseuscommand.h
++++ mothur-1.23.1/chimeraperseuscommand.h
+@@ -98,7 +98,7 @@
+ }
+ };
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
+ perseusData* pDataArray;
+--- mothur-1.23.1.orig/chimerapintailcommand.cpp
++++ mothur-1.23.1/chimerapintailcommand.cpp
+@@ -697,7 +697,7 @@
+
+ int ChimeraPintailCommand::createProcesses(string outputFileName, string filename, string accnos) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
+ int num = 0;
+
+--- mothur-1.23.1.orig/chimeraslayercommand.cpp
++++ mothur-1.23.1/chimeraslayercommand.cpp
+@@ -495,14 +495,14 @@
+ else {
+ //add / to name if needed
+ string lastChar = blastlocation.substr(blastlocation.length()-1);
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if (lastChar != "/") { blastlocation += "/"; }
+ #else
+ if (lastChar != "\\") { blastlocation += "\\"; }
+ #endif
+ blastlocation = m->getFullPathName(blastlocation);
+ string formatdbCommand = "";
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ formatdbCommand = blastlocation + "formatdb";
+ #else
+ formatdbCommand = blastlocation + "formatdb.exe";
+@@ -515,7 +515,7 @@
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
+
+ string blastCommand = "";
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ blastCommand = blastlocation + "megablast";
+ #else
+ blastCommand = blastlocation + "megablast.exe";
+@@ -533,7 +533,7 @@
+ if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
+
+ //until we resolve the issue 10-18-11
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ //processors=1;
+ #endif
+@@ -594,7 +594,7 @@
+ #else
+ //break up file
+ vector<unsigned long long> positions;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ positions = m->divideFile(thisFastaName, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+ #else
+@@ -1187,7 +1187,7 @@
+ m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine();
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
---- mothur-1.22.2.orig/chimerauchimecommand.cpp
-+++ mothur-1.22.2/chimerauchimecommand.cpp
+ lines.clear();
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int proc = 1;
+ vector<unsigned long long> positions = m->divideFile(thisFastaName, proc);
+ lines.push_back(linePair(positions[0], positions[1]));
+@@ -1244,7 +1244,7 @@
+ breakUp.push_back(thisFileToPriority);
+ }
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+@@ -1628,7 +1628,7 @@
+ int num = 0;
+ processIDS.clear();
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+--- mothur-1.23.1.orig/chimeraslayercommand.h
++++ mothur-1.23.1/chimeraslayercommand.h
+@@ -172,7 +172,7 @@
+ };
+
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
+ slayerData* pDataArray;
+--- mothur-1.23.1.orig/chimerauchimecommand.cpp
++++ mothur-1.23.1/chimerauchimecommand.cpp
@@ -461,7 +461,7 @@
path = path.substr(0, (tempPath.find_last_of('m')));
@@ -82,43 +284,34 @@
uchimeCommand = path + "uchime"; // format the database, -o option gives us the ability
#else
uchimeCommand = path + "uchime.exe";
-@@ -543,7 +543,7 @@
- if (chimealns) { m->openOutputFile(alnsFileName, out2); out2.close(); }
- int totalSeqs = 0;
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1) { totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups); }
- else { totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups); }
- #else
-@@ -563,7 +563,7 @@
-
- int numSeqs = 0;
- int numChimeras = 0;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
- else{ numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
- #else
-@@ -990,7 +990,7 @@
- vector<char*> cPara;
-
- char* tempUchime;
+@@ -1005,7 +1005,7 @@
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+ string uchimeCommand = path;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- tempUchime= new char[10];
- *tempUchime = '\0';
- strncat(tempUchime, "./uchime ", 9);
-@@ -1286,7 +1286,7 @@
- processIDS.clear();
- int process = 1;
+ uchimeCommand += "uchime ";
+ #else
+ uchimeCommand += "uchime";
+@@ -1243,7 +1243,7 @@
+
+ //uchime_main(numArgs, uchimeParameters);
+ //cout << "commandString = " << commandString << endl;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ commandString = "\"" + commandString + "\"";
+ #endif
+@@ -1309,7 +1309,7 @@
int num = 0;
+ vector<string> files;
+
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
//break up file into multiple files
- vector<string> files;
m->divideFile(filename, processors, files);
-@@ -1389,7 +1389,7 @@
+
+@@ -1492,7 +1492,7 @@
lines.push_back(linePair(startIndex, endIndex));
}
@@ -127,64 +320,141 @@
//loop through and create all the processes you want
while (process != processors) {
---- mothur-1.22.2.orig/trimseqscommand.cpp
-+++ mothur-1.22.2/trimseqscommand.cpp
-@@ -363,7 +363,7 @@
- }
- if(qFileName == "") { qLines = lines; } //files with duds
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
- }else{
-@@ -723,7 +723,7 @@
- count++;
- }
+--- mothur-1.23.1.orig/chimerauchimecommand.h
++++ mothur-1.23.1/chimerauchimecommand.h
+@@ -141,7 +141,7 @@
+ };
+
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
+ uchimeData* pDataArray;
+@@ -189,7 +189,7 @@
+ path = path.substr(0, (tempPath.find_last_of('m')));
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= line->end)) { break; }
+ string uchimeCommand = path;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ uchimeCommand += "uchime ";
+ #else
+ uchimeCommand += "uchime";
+@@ -403,7 +403,7 @@
-@@ -758,7 +758,7 @@
+ //uchime_main(numArgs, uchimeParameters);
+ //cout << "commandString = " << commandString << endl;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ commandString = "\"" + commandString + "\"";
+ #endif
+--- mothur-1.23.1.orig/classifyseqscommand.cpp
++++ mothur-1.23.1/classifyseqscommand.cpp
+@@ -594,7 +594,7 @@
+ #else
+
+ vector<unsigned long long> positions;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ positions = m->divideFile(fastaFileNames[s], processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
+ #else
+@@ -791,7 +791,7 @@
+ int num = 0;
+ processIDS.clear();
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+
+ //loop through and create all the processes you want
+--- mothur-1.23.1.orig/classifyseqscommand.h
++++ mothur-1.23.1/classifyseqscommand.h
+@@ -128,7 +128,7 @@
+ };
- int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
+ classifyData* pDataArray;
+--- mothur-1.23.1.orig/distancecommand.cpp
++++ mothur-1.23.1/distancecommand.cpp
+@@ -507,7 +507,7 @@
+ /**************************************************************************************************/
+ void DistanceCommand::createProcesses(string filename) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
int process = 1;
- int exitCommand = 1;
processIDS.clear();
-@@ -942,7 +942,7 @@
+
+--- mothur-1.23.1.orig/distancecommand.h
++++ mothur-1.23.1/distancecommand.h
+@@ -53,7 +53,7 @@
+ };
- int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long long>& fastaFilePos, vector<unsigned long long>& qfileFilePos) {
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
+ distanceData* pDataArray;
+--- mothur-1.23.1.orig/filterseqscommand.cpp
++++ mothur-1.23.1/filterseqscommand.cpp
+@@ -598,7 +598,7 @@
+
+ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
try {
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- //set file positions for fasta file
- fastaFilePos = m->divideFile(filename, processors);
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
+ int num = 0;
+ processIDS.clear();
+@@ -954,7 +954,7 @@
+
+ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ int num = 0;
+ processIDS.clear();
+--- mothur-1.23.1.orig/indicatorcommand.cpp
++++ mothur-1.23.1/indicatorcommand.cpp
+@@ -1120,7 +1120,7 @@
+ try {
+ vector<float> pvalues;
---- mothur-1.22.2.orig/mothurout.cpp
-+++ mothur-1.22.2/mothurout.cpp
-@@ -143,7 +143,7 @@
-
- //add / to name if needed
- string lastChar = pathname.substr(pathname.length()-1);
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if (lastChar != "/") { pathname += "/"; }
- #else
- if (lastChar != "\\") { pathname += "\\"; }
-@@ -332,7 +332,7 @@
- //
- // On failure, returns 0.0, 0.0
- int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
-
- vm_usage = 0.0;
- resident_set = 0.0;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+@@ -1234,7 +1234,7 @@
+ try {
+ vector<float> pvalues;
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+--- mothur-1.23.1.orig/mothur.h
++++ mothur-1.23.1/mothur.h
+@@ -53,7 +53,7 @@
+ #endif
+ /***********************************************************************/
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #include <sys/wait.h>
+ #include <sys/time.h>
+ #include <sys/resource.h>
+--- mothur-1.23.1.orig/mothurout.cpp
++++ mothur-1.23.1/mothurout.cpp
@@ -504,7 +504,7 @@
}
/***********************************************************************/
@@ -203,15 +473,6 @@
#ifdef USE_COMPRESSION
if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
int pos = rootName.find_last_of('.');
-@@ -673,7 +673,7 @@
-
- string cwd;
- //get current working directory
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
-
- if (path.find("~") != -1) { //go to home directory
- string homeDir;
@@ -796,7 +796,7 @@
try {
//get full path name
@@ -230,15 +491,6 @@
#ifdef USE_COMPRESSION
// check for gzipped or bzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
-@@ -893,7 +893,7 @@
- int exist = openInputFile(newName, inTest, "");
- inTest.close();
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if (exist == 0) { //you could open it so you want to delete it
- string command = "rm " + newName;
- system(command.c_str());
@@ -920,7 +920,7 @@
try {
@@ -248,55 +500,97 @@
#ifdef USE_COMPRESSION
// check for gzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
-@@ -996,7 +996,7 @@
+--- mothur-1.23.1.orig/myseqdist.cpp
++++ mothur-1.23.1/myseqdist.cpp
+@@ -46,7 +46,7 @@
+ /**************************************************************************************************/
+ int correctDist::execute(string distanceFileName){
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ processors = 1;
+ #endif
+@@ -146,7 +146,7 @@
+ int correctDist::createProcess(string distanceFileName){
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ vector<int> processIDs;
- //if you can, use the unix sort since its been optimized for years
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- string command = "sort -n -k +3 " + distFile + " -o " + outfile;
- system(command.c_str());
- #else //you are stuck with my best attempt...
---- mothur-1.22.2.orig/setdircommand.cpp
-+++ mothur-1.22.2/setdircommand.cpp
-@@ -114,7 +114,7 @@
- }else {
- //add / to name if needed
- string lastChar = output.substr(output.length()-1);
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if (lastChar != "/") { output += "/"; }
- #else
- if (lastChar != "\\") { output += "\\"; }
-@@ -146,7 +146,7 @@
- }else {
- //add / to name if needed
- string lastChar = input.substr(input.length()-1);
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if (lastChar != "/") { input += "/"; }
- #else
- if (lastChar != "\\") { input += "\\"; }
-@@ -188,7 +188,7 @@
- }else {
- //add / to name if needed
- string lastChar = tempdefault.substr(tempdefault.length()-1);
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if (lastChar != "/") { tempdefault += "/"; }
- #else
- if (lastChar != "\\") { tempdefault += "\\"; }
---- mothur-1.22.2.orig/pintail.cpp
-+++ mothur-1.22.2/pintail.cpp
-@@ -74,7 +74,7 @@
- #ifdef USE_MPI
- //do nothing
- #else
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- //find breakup of templatefile for quantiles
- if (processors == 1) { templateLines.push_back(new linePair(0, templateSeqs.size())); }
- else {
+--- mothur-1.23.1.orig/myutils.cpp
++++ mothur-1.23.1/myutils.cpp
+@@ -11,7 +11,7 @@
+ #include <signal.h>
+ #include <float.h>
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #include <sys/time.h>
+ #include <sys/resource.h>
+ #include <unistd.h>
+@@ -139,7 +139,7 @@
+ return isatty(fd) != 0;
+ }
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ //#ifdef BIT_VERSION
+ //#include <io.h>
+@@ -176,7 +176,7 @@
+ Log("fpos %ld (retval %d)\n", (long) fpos, fgetpos_retval);
+ // Log("eof %d\n", _eof(fd));
+ #endif
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ #ifdef BIT_VERSION
+ __int64 pos64 = _ftelli64(f);
+@@ -612,7 +612,7 @@
+ fprintf(stderr, "\n---Fatal error---\n%s\n", szStr);
+ Log("\n---Fatal error---\n%s\n", szStr);
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ //if (IsDebuggerPresent())
+ // __debugbreak();
+@@ -1205,7 +1205,7 @@
+ g_Opts.insert(Opt);
+ }
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ #pragma warning(disable: 4505) // unreferenced local function
+ #endif
+--- mothur-1.23.1.orig/pairwiseseqscommand.cpp
++++ mothur-1.23.1/pairwiseseqscommand.cpp
+@@ -535,7 +535,7 @@
+ /**************************************************************************************************/
+ void PairwiseSeqsCommand::createProcesses(string filename) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ processIDS.clear();
+
+--- mothur-1.23.1.orig/parsimony.cpp
++++ mothur-1.23.1/parsimony.cpp
+@@ -91,7 +91,7 @@
+
+ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ vector<int> processIDS;
+
+--- mothur-1.23.1.orig/pintail.cpp
++++ mothur-1.23.1/pintail.cpp
@@ -529,7 +529,7 @@
//**************************************************************************************************
void Pintail::createProcessesQuan() {
@@ -306,37 +600,70 @@
int process = 1;
vector<int> processIDS;
---- mothur-1.22.2.orig/chimeraccodecommand.cpp
-+++ mothur-1.22.2/chimeraccodecommand.cpp
-@@ -397,7 +397,7 @@
- }
-
- //break up file
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
-
- numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
-@@ -521,7 +521,7 @@
- }
- delete candidateSeq;
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
-@@ -608,7 +608,7 @@
+--- mothur-1.23.1.orig/preclustercommand.cpp
++++ mothur-1.23.1/preclustercommand.cpp
+@@ -299,7 +299,7 @@
+ lines.push_back(linePair(startIndex, endIndex));
+ }
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+--- mothur-1.23.1.orig/preclustercommand.h
++++ mothur-1.23.1/preclustercommand.h
+@@ -113,7 +113,7 @@
+ };
- int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
+ preClusterData* pDataArray;
+--- mothur-1.23.1.orig/rarefact.cpp
++++ mothur-1.23.1/rarefact.cpp
+@@ -114,7 +114,7 @@
+
+ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd, int increment) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+
+ vector<int> processIDS;
+--- mothur-1.23.1.orig/screenseqscommand.cpp
++++ mothur-1.23.1/screenseqscommand.cpp
+@@ -664,7 +664,7 @@
+ vector<int> ambigBases;
+ vector<int> longHomoPolymer;
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ vector<unsigned long long> positions = m->divideFile(fastafile, processors);
+
+ for (int i = 0; i < (positions.size()-1); i++) {
+@@ -808,7 +808,7 @@
+ /**************************************************************************************************/
+ int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ int num = 0;
+ processIDS.clear();
+@@ -1270,7 +1270,7 @@
+
+ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
int process = 0;
int num = 0;
---- mothur-1.22.2.orig/seqerrorcommand.cpp
-+++ mothur-1.22.2/seqerrorcommand.cpp
+--- mothur-1.23.1.orig/seqerrorcommand.cpp
++++ mothur-1.23.1/seqerrorcommand.cpp
@@ -293,7 +293,7 @@
if(qualFileName == "") { qLines = lines; rLines = lines; } //fills with duds
@@ -355,15 +682,6 @@
//loop through and create all the processes you want
while (process != processors) {
-@@ -734,7 +734,7 @@
-
- index++;
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = queryFile.tellg();
- if ((pos == -1) || (pos >= line.end)) { break; }
- #else
@@ -1210,7 +1210,7 @@
int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long long>& fastaFilePos, vector<unsigned long long>& qfileFilePos, vector<unsigned long long>& rfileFilePos) {
@@ -373,124 +691,8 @@
//set file positions for fasta file
fastaFilePos = m->divideFile(filename, processors);
---- mothur-1.22.2.orig/filterseqscommand.cpp
-+++ mothur-1.22.2/filterseqscommand.cpp
-@@ -425,7 +425,7 @@
- for (int i = 0; i < (positions.size()-1); i++) {
- lines.push_back(new linePair(positions[i], positions[(i+1)]));
- }
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
- numSeqs += numFastaSeqs;
-@@ -567,7 +567,7 @@
- count++;
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = in.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
-@@ -595,7 +595,7 @@
-
- int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
- try {
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 0;
- int num = 0;
- processIDS.clear();
-@@ -741,7 +741,7 @@
- for (int i = 0; i < (positions.size()-1); i++) {
- lines.push_back(new linePair(positions[i], positions[(i+1)]));
- }
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
- numSeqs += numFastaSeqs;
-@@ -876,7 +876,7 @@
- count++;
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = in.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
-@@ -948,7 +948,7 @@
-
- int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
- try {
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 1;
- int num = 0;
- processIDS.clear();
---- mothur-1.22.2.orig/trimflowscommand.h
-+++ mothur-1.22.2/trimflowscommand.h
-@@ -130,7 +130,7 @@
- };
-
- /**************************************************************************************************/
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- #else
- static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
- trimFlowData* pDataArray;
---- mothur-1.22.2.orig/distancecommand.h
-+++ mothur-1.22.2/distancecommand.h
-@@ -53,7 +53,7 @@
- };
-
- /**************************************************************************************************/
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- #else
- static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
- distanceData* pDataArray;
---- mothur-1.22.2.orig/indicatorcommand.cpp
-+++ mothur-1.22.2/indicatorcommand.cpp
-@@ -1120,7 +1120,7 @@
- try {
- vector<float> pvalues;
-
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
- for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
-@@ -1234,7 +1234,7 @@
- try {
- vector<float> pvalues;
-
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
- for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
---- mothur-1.22.2.orig/seqsummarycommand.cpp
-+++ mothur-1.22.2/seqsummarycommand.cpp
-@@ -282,7 +282,7 @@
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- #else
- vector<unsigned long long> positions;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- positions = m->divideFile(fastafile, processors);
- for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
- #else
-@@ -429,7 +429,7 @@
- outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = in.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
+--- mothur-1.23.1.orig/seqsummarycommand.cpp
++++ mothur-1.23.1/seqsummarycommand.cpp
@@ -525,7 +525,7 @@
int num = 0;
processIDS.clear();
@@ -500,157 +702,19 @@
//loop through and create all the processes you want
while (process != processors) {
---- mothur-1.22.2.orig/clustersplitcommand.cpp
-+++ mothur-1.22.2/clustersplitcommand.cpp
-@@ -559,7 +559,7 @@
- //sanity check
- if (processors > distName.size()) { processors = distName.size(); }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
- }else{
-@@ -907,7 +907,7 @@
- int ClusterSplitCommand::createProcesses(vector < vector < map<string, string> > > dividedNames){
- try {
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 0;
- int exitCommand = 1;
- processIDS.clear();
---- mothur-1.22.2.orig/formatphylip.cpp
-+++ mothur-1.22.2/formatphylip.cpp
+--- mothur-1.23.1.orig/seqsummarycommand.h
++++ mothur-1.23.1/seqsummarycommand.h
@@ -96,7 +96,7 @@
- string outfile = m->getRootName(tempFile) + "sorted.dist.temp";
-
- //use the unix sort
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- string command = "sort -n " + tempFile + " -o " + outfile;
- system(command.c_str());
- #else //sort using windows sort
---- mothur-1.22.2.orig/mothur.h
-+++ mothur-1.22.2/mothur.h
-@@ -53,7 +53,7 @@
- #endif
- /***********************************************************************/
-
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- #include <sys/wait.h>
- #include <sys/time.h>
- #include <sys/resource.h>
---- mothur-1.22.2.orig/engine.cpp
-+++ mothur-1.22.2/engine.cpp
-@@ -34,7 +34,7 @@
-
- //delimiting path char
- char delim;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- delim = ':';
- #else
- delim = ';';
-@@ -56,7 +56,7 @@
-
- if (mothurPath != "") {
- //add mothur so it looks like what argv would look like
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- mothurPath += "/mothur";
- #else
- mothurPath += "\\mothur";
-@@ -71,7 +71,7 @@
- //is this mothurs path?
- ifstream in;
- string tempIn = dirs[i];
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- tempIn += "/mothur";
- #else
- tempIn += "\\mothur";
-@@ -217,7 +217,7 @@
- string Engine::getCommand() {
- try {
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- #ifdef USE_READLINE
- char* nextCommand = NULL;
- nextCommand = readline("mothur > ");
---- mothur-1.22.2.orig/bellerophon.cpp
-+++ mothur-1.22.2/bellerophon.cpp
-@@ -314,7 +314,7 @@
- #else
-
- //divide breakpoints between processors
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- lines.push_back(linePair(0, iters));
-
-@@ -356,7 +356,7 @@
-
- int Bellerophon::createProcesses(vector<int> mid) {
- try {
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 0;
- int exitCommand = 1;
- vector<int> processIDS;
---- mothur-1.22.2.orig/aligncommand.h
-+++ mothur-1.22.2/aligncommand.h
-@@ -118,7 +118,7 @@
};
/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
#else
- static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
- alignData* pDataArray;
---- mothur-1.22.2.orig/catchallcommand.cpp
-+++ mothur-1.22.2/catchallcommand.cpp
-@@ -176,7 +176,7 @@
-
- savedOutputDir = outputDir;
- string catchAllCommandExe = "";
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
- if (outputDir == "") { outputDir = "./"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
- #else
-@@ -224,7 +224,7 @@
-
- //create system command
- string catchAllCommand = "";
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
- #else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
-@@ -269,7 +269,7 @@
-
- //create system command
- string catchAllCommand = "";
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
- #else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
-@@ -334,7 +334,7 @@
-
- //create system command
- string catchAllCommand = "";
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
- #else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
---- mothur-1.22.2.orig/shhhercommand.cpp
-+++ mothur-1.22.2/shhhercommand.cpp
+ static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
+ seqSumData* pDataArray;
+--- mothur-1.23.1.orig/shhhercommand.cpp
++++ mothur-1.23.1/shhhercommand.cpp
@@ -1211,7 +1211,7 @@
string ShhherCommand::createDistFile(int processors){
try{
@@ -669,7 +733,7 @@
//loop through and create all the processes you want
while (process != processors) {
-@@ -1556,7 +1556,7 @@
+@@ -1555,7 +1555,7 @@
void ShhherCommand::calcCentroids(){
try{
@@ -678,7 +742,7 @@
if(processors == 1) {
calcCentroidsDriver(0, numOTUs);
-@@ -1829,7 +1829,7 @@
+@@ -1828,7 +1828,7 @@
void ShhherCommand::calcNewDistances(){
try{
@@ -687,532 +751,134 @@
if(processors == 1) {
calcNewDistancesParent(0, numSeqs);
---- mothur-1.22.2.orig/seqsummarycommand.h
-+++ mothur-1.22.2/seqsummarycommand.h
-@@ -96,7 +96,7 @@
+--- mothur-1.23.1.orig/shhhercommand.h
++++ mothur-1.23.1/shhhercommand.h
+@@ -160,7 +160,7 @@
};
/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
#else
- static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
- seqSumData* pDataArray;
---- mothur-1.22.2.orig/metastatscommand.cpp
-+++ mothur-1.22.2/metastatscommand.cpp
-@@ -233,7 +233,7 @@
- if (numGroups == 2) { processors = 1; }
- else if (numGroups < 2) { m->mothurOut("Not enough sets, I need at least 2 valid sets. Unable to complete command."); m->mothurOutEndLine(); m->control_pressed = true; }
+ static DWORD WINAPI MyflowDistParentForkThreadFunction(LPVOID lpParam){
+ flowDistParentForkData* pDataArray;
+--- mothur-1.23.1.orig/shhhseqscommand.cpp
++++ mothur-1.23.1/shhhseqscommand.cpp
+@@ -358,7 +358,7 @@
+ lines.push_back(linePair(startIndex, endIndex));
+ }
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors != 1){
- int numPairs = namesOfGroupCombos.size();
- int numPairsPerProcessor = numPairs / processors;
-@@ -339,7 +339,7 @@
- int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
- try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- driver(0, namesOfGroupCombos.size(), thisLookUp);
- }else{
---- mothur-1.22.2.orig/distancecommand.cpp
-+++ mothur-1.22.2/distancecommand.cpp
-@@ -380,7 +380,7 @@
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- #else
-
-- //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ //#if defined (__APPLE__) || (__MACH__) || (__unix__)
- //if you don't need to fork anything
- if(processors == 1){
- if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
-@@ -507,7 +507,7 @@
+ //loop through and create all the processes you want
+ while (process != processors) {
+--- mothur-1.23.1.orig/shhhseqscommand.h
++++ mothur-1.23.1/shhhseqscommand.h
+@@ -97,7 +97,7 @@
+ };
+
/**************************************************************************************************/
- void DistanceCommand::createProcesses(string filename) {
- try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 1;
- processIDS.clear();
-
-@@ -1014,7 +1014,7 @@
- string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
-
- //use the unix sort
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- string command = "sort -n " + outputFile + " -o " + outfile;
- system(command.c_str());
- #else //sort using windows sort
-@@ -1102,7 +1102,7 @@
- string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
-
- //use the unix sort
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- string command = "sort -n " + outputFile + " -o " + outfile;
- system(command.c_str());
- #else //sort using windows sort
---- mothur-1.22.2.orig/aligncommand.cpp
-+++ mothur-1.22.2/aligncommand.cpp
-@@ -248,7 +248,7 @@
- temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
- save = m->isTrue(temp);
- //this is so the threads can quickly load the reference data
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- #else
- if (processors != 1) { save = true; }
- #endif
-@@ -427,7 +427,7 @@
#else
-
- vector<unsigned long long> positions;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- positions = m->divideFile(candidateFileNames[s], processors);
- for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
- #else
-@@ -622,7 +622,7 @@
+ static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){
+ shhhseqsData* pDataArray;
+--- mothur-1.23.1.orig/summaryqualcommand.cpp
++++ mothur-1.23.1/summaryqualcommand.cpp
+@@ -157,7 +157,7 @@
+ if (namefile != "") { nameMap = m->readNames(namefile); }
+
+ vector<unsigned long long> positions;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ positions = m->divideFile(qualfile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+ #else
+@@ -262,7 +262,7 @@
+ count += num;
}
- delete candidateSeq;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
-@@ -831,7 +831,7 @@
- try {
- int num = 0;
- processIDS.resize(0);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 1;
-
- //loop through and create all the processes you want
---- mothur-1.22.2.orig/pairwiseseqscommand.cpp
-+++ mothur-1.22.2/pairwiseseqscommand.cpp
-@@ -444,7 +444,7 @@
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- #else
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- //if you don't need to fork anything
- if(processors == 1){
- if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
-@@ -535,7 +535,7 @@
- /**************************************************************************************************/
- void PairwiseSeqsCommand::createProcesses(string filename) {
- try {
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 1;
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos.end)) { break; }
+ #else
+@@ -286,7 +286,7 @@
+ int numSeqs = 0;
processIDS.clear();
---- mothur-1.22.2.orig/rarefact.cpp
-+++ mothur-1.22.2/rarefact.cpp
-@@ -24,7 +24,7 @@
- if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
- else { increment = percentFreq; }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- driver(rcd, increment, nIters);
- }else{
-@@ -114,7 +114,7 @@
-
- int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd, int increment) {
- try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 1;
- vector<int> processIDS;
---- mothur-1.22.2.orig/matrixoutputcommand.cpp
-+++ mothur-1.22.2/matrixoutputcommand.cpp
-@@ -459,7 +459,7 @@
- vector<SharedRAbundVector*> subset;
- vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size()); //one for each calc, this will be used to make .dist files
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- driver(thisLookup, 0, numGroups, calcDists);
- }else{
---- mothur-1.22.2.orig/unifracweightedcommand.cpp
-+++ mothur-1.22.2/unifracweightedcommand.cpp
-@@ -337,7 +337,7 @@
-
- lines.clear();
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors != 1){
- int numPairs = namesOfGroupCombos.size();
- int numPairsPerProcessor = numPairs / processors;
-@@ -356,7 +356,7 @@
- //get scores for random trees
- for (int j = 0; j < iters; j++) {
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
- }else{
-@@ -454,7 +454,7 @@
+ //loop through and create all the processes you want
+ while (process != processors) {
+--- mothur-1.23.1.orig/summaryqualcommand.h
++++ mothur-1.23.1/summaryqualcommand.h
+@@ -84,7 +84,7 @@
+ };
- int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector< vector<double> >& scores) {
- try {
+ /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 1;
- vector<int> processIDS;
-
---- mothur-1.22.2.orig/summarysharedcommand.cpp
-+++ mothur-1.22.2/summarysharedcommand.cpp
-@@ -511,7 +511,7 @@
- vector< vector<seqDist> > calcDists; //vector containing vectors that contains the summary results for each group compare
- calcDists.resize(sumCalculators.size()); //one for each calc, this will be used to make .dist files
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
- m->appendFiles((sumFileName + ".temp"), sumFileName);
---- mothur-1.22.2.orig/chimeraslayercommand.cpp
-+++ mothur-1.22.2/chimeraslayercommand.cpp
-@@ -495,14 +495,14 @@
- else {
- //add / to name if needed
- string lastChar = blastlocation.substr(blastlocation.length()-1);
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- if (lastChar != "/") { blastlocation += "/"; }
#else
- if (lastChar != "\\") { blastlocation += "\\"; }
- #endif
- blastlocation = m->getFullPathName(blastlocation);
- string formatdbCommand = "";
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- formatdbCommand = blastlocation + "formatdb";
- #else
- formatdbCommand = blastlocation + "formatdb.exe";
-@@ -515,7 +515,7 @@
- if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
-
- string blastCommand = "";
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- blastCommand = blastlocation + "megablast";
- #else
- blastCommand = blastlocation + "megablast.exe";
-@@ -533,7 +533,7 @@
- if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
+ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
+ seqSumQualData* pDataArray;
+--- mothur-1.23.1.orig/trimflowscommand.cpp
++++ mothur-1.23.1/trimflowscommand.cpp
+@@ -447,7 +447,7 @@
+ //report progress
+ if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
- //until we resolve the issue 10-18-11
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- #else
- processors=1;
- #endif
-@@ -644,7 +644,7 @@
- //create chimera here if you are mac or linux because fork will copy for you. Create in create processes instead if you are windows.
- if (processors == 1) { templateSeqsLength = setupChimera(thisFastaName, thisPriority); }
- else {
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__) || USE_MPI
- templateSeqsLength = setupChimera(thisFastaName, thisPriority);
- #endif
- }
-@@ -657,7 +657,7 @@
- #else
- //break up file
- vector<unsigned long long> positions;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- positions = m->divideFile(thisFastaName, processors);
- for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
- #else
-@@ -687,7 +687,7 @@
-
- #endif
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__) || USE_MPI
- delete chimera;
- #endif
-
-@@ -1197,7 +1197,7 @@
- count++;
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
-@@ -1358,7 +1358,7 @@
- int numNoParents = 0;
+ unsigned long long pos = flowFile.tellg();
+
+ if ((pos == -1) || (pos >= line->end)) { break; }
+@@ -688,7 +688,7 @@
processIDS.clear();
+ int exitCommand = 1;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- //loop through and create all the processes you want
- while (process != processors) {
- int pid = fork();
---- mothur-1.22.2.orig/screenseqscommand.cpp
-+++ mothur-1.22.2/screenseqscommand.cpp
-@@ -390,7 +390,7 @@
-
- #else
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
-
-@@ -645,7 +645,7 @@
- }
-
- int numSeqs = 0;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
- }else{
-@@ -723,7 +723,7 @@
- count++;
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = in.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
-@@ -744,7 +744,7 @@
- /**************************************************************************************************/
- int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
- try {
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
int process = 1;
- int num = 0;
- processIDS.clear();
-@@ -1049,7 +1049,7 @@
- count++;
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
-@@ -1156,7 +1156,7 @@
-
- int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
- try {
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 0;
- int num = 0;
---- mothur-1.22.2.orig/chimeraslayercommand.h
-+++ mothur-1.22.2/chimeraslayercommand.h
-@@ -135,7 +135,7 @@
+ //loop through and create all the processes you want
+--- mothur-1.23.1.orig/trimflowscommand.h
++++ mothur-1.23.1/trimflowscommand.h
+@@ -130,7 +130,7 @@
};
/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
#else
- static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
- slayerData* pDataArray;
---- mothur-1.22.2.orig/weighted.cpp
-+++ mothur-1.22.2/weighted.cpp
-@@ -34,7 +34,7 @@
- }
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
- }else{
-@@ -69,7 +69,7 @@
+ static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
+ trimFlowData* pDataArray;
+--- mothur-1.23.1.orig/trimseqscommand.cpp
++++ mothur-1.23.1/trimseqscommand.cpp
+@@ -758,7 +758,7 @@
- EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
int process = 1;
- vector<int> processIDS;
-
---- mothur-1.22.2.orig/chimeracheckcommand.cpp
-+++ mothur-1.22.2/chimeracheckcommand.cpp
-@@ -431,7 +431,7 @@
- }
-
- //break up file
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
-
-@@ -519,7 +519,7 @@
- }
- delete candidateSeq;
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
-@@ -596,7 +596,7 @@
+ int exitCommand = 1;
+ processIDS.clear();
+--- mothur-1.23.1.orig/unifracweightedcommand.cpp
++++ mothur-1.23.1/unifracweightedcommand.cpp
+@@ -454,7 +454,7 @@
- int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
+ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector< vector<double> >& scores) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 0;
- int num = 0;
+ int process = 1;
+ vector<int> processIDS;
---- mothur-1.22.2.orig/blastdb.cpp
-+++ mothur-1.22.2/blastdb.cpp
-@@ -24,7 +24,7 @@
- int randNumber = rand();
- //int randNumber = 12345;
- string pid = "";
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- pid += getpid();
- #else
- pid += toString(threadID);
-@@ -42,7 +42,7 @@
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
-
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- path += "blast/bin/";
- #else
- path += "blast\\bin\\";
-@@ -51,7 +51,7 @@
-
-
- string formatdbCommand;
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
- #else
- formatdbCommand = path + "formatdb.exe";
-@@ -64,7 +64,7 @@
- if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
-
- string blastCommand;
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- blastCommand = path + "blastall"; // format the database, -o option gives us the ability
- #else
- blastCommand = path + "blastall.exe";
-@@ -80,7 +80,7 @@
-
-
- string megablastCommand;
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
- #else
- megablastCommand = path + "megablast.exe";
-@@ -114,7 +114,7 @@
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
-
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- path += "blast/bin/";
- #else
- path += "blast\\bin\\";
-@@ -123,7 +123,7 @@
-
- int randNumber = rand();
- string pid = "";
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- pid += getpid();
- #else
- pid += toString(threadID);
-@@ -134,7 +134,7 @@
- blastFileName = pid + toString(randNumber) + ".blast";
-
- string formatdbCommand;
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
- #else
- formatdbCommand = path + "formatdb.exe";
-@@ -149,7 +149,7 @@
- if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
-
- string blastCommand;
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- blastCommand = path + "blastall"; // format the database, -o option gives us the ability
- #else
- blastCommand = path + "blastall.exe";
-@@ -165,7 +165,7 @@
-
-
- string megablastCommand;
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
- #else
- megablastCommand = path + "megablast.exe";
-@@ -226,7 +226,7 @@
- // long. With this setting, it seems comparable in speed to the suffix tree approach.
-
- string blastCommand;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
-
- blastCommand = path + "blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
- blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
-@@ -289,7 +289,7 @@
- // long. With this setting, it seems comparable in speed to the suffix tree approach.
- //7000004128189528left 0 100 66 0 0 1 66 61 126 1e-31 131
- string blastCommand;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- blastCommand = path + "megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
- blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
- #else
-@@ -363,7 +363,7 @@
-
- string formatdbCommand;
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- formatdbCommand = path + "formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
- #else
- //formatdbCommand = path + "blast\\bin\\formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
---- mothur-1.22.2.orig/unweighted.cpp
-+++ mothur-1.22.2/unweighted.cpp
-@@ -48,7 +48,7 @@
- }
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
- }else{
+--- mothur-1.23.1.orig/unweighted.cpp
++++ mothur-1.23.1/unweighted.cpp
@@ -83,7 +83,7 @@
EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
@@ -1222,15 +888,6 @@
int process = 1;
vector<int> processIDS;
-@@ -291,7 +291,7 @@
- }
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
- }else{
@@ -326,7 +326,7 @@
EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
@@ -1240,154 +897,14 @@
int process = 1;
vector<int> processIDS;
---- mothur-1.22.2.orig/chimerapintailcommand.cpp
-+++ mothur-1.22.2/chimerapintailcommand.cpp
-@@ -493,7 +493,7 @@
- }
-
- //break up file
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
-
- numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
-@@ -609,7 +609,7 @@
- }
- delete candidateSeq;
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
-@@ -695,7 +695,7 @@
+--- mothur-1.23.1.orig/weighted.cpp
++++ mothur-1.23.1/weighted.cpp
+@@ -69,7 +69,7 @@
- int ChimeraPintailCommand::createProcesses(string outputFileName, string filename, string accnos) {
+ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 0;
- int num = 0;
-
---- mothur-1.22.2.orig/formatcolumn.cpp
-+++ mothur-1.22.2/formatcolumn.cpp
-@@ -82,7 +82,7 @@
- string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
-
- //use the unix sort
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- string command = "sort -n " + squareFile + " -o " + outfile;
- system(command.c_str());
- #else //sort using windows sort
---- mothur-1.22.2.orig/shhhercommand.h
-+++ mothur-1.22.2/shhhercommand.h
-@@ -160,7 +160,7 @@
- };
-
- /**************************************************************************************************/
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- #else
- static DWORD WINAPI MyflowDistParentForkThreadFunction(LPVOID lpParam){
- flowDistParentForkData* pDataArray;
---- mothur-1.22.2.orig/mothur.cpp
-+++ mothur-1.22.2/mothur.cpp
-@@ -46,7 +46,7 @@
-
- m->setFileName(logFileName);
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- system("clear");
- #else
- system("CLS");
-@@ -57,7 +57,7 @@
-
- //add / to name if needed
- string lastChar = temp.substr(temp.length()-1);
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if (lastChar != "/") { temp += "/"; }
- #else
- if (lastChar != "\\") { temp += "\\"; }
-@@ -88,7 +88,7 @@
-
- if (outputHeader) {
- //version
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- #if defined (__APPLE__) || (__MACH__)
- m->mothurOutJustToLog("Mac version");
- m->mothurOutEndLine(); m->mothurOutEndLine();
---- mothur-1.22.2.orig/phylodiversitycommand.cpp
-+++ mothur-1.22.2/phylodiversitycommand.cpp
-@@ -348,7 +348,7 @@
- if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) { numSampledList.insert(diversity[mGroups[j]].size()-1); }
- }
-
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- if(processors == 1){
- driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
- }else{
-@@ -398,7 +398,7 @@
- //**********************************************************************************************************************
- int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map< string, vector<float> >& div, map<string, vector<float> >& sumDiv, int numIters, int increment, vector<int>& randomLeaf, set<int>& numSampledList, ofstream& outCollect, ofstream& outSum){
- try {
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
int process = 1;
-
vector<int> processIDS;
---- mothur-1.22.2.orig/endiannessmacros.h
-+++ mothur-1.22.2/endiannessmacros.h
-@@ -125,7 +125,7 @@
- * out at over 2-times faster than iswap_int4 above.
- */
- #if 0
--#if defined(__linux__)
-+#if defined(__GLIBC____)
- # include <byteswap.h>
- # undef iswap_int8
- # undef iswap_int4
---- mothur-1.22.2.orig/trimflowscommand.cpp
-+++ mothur-1.22.2/trimflowscommand.cpp
-@@ -226,7 +226,7 @@
- }
- vector<unsigned long long> flowFilePos;
-- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+ #if defined (__APPLE__) || (__MACH__) || (__unix__)
- flowFilePos = getFlowFileBreaks();
- for (int i = 0; i < (flowFilePos.size()-1); i++) {
- lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
-@@ -445,7 +445,7 @@
- //report progress
- if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- unsigned long long pos = flowFile.tellg();
-
- if ((pos == -1) || (pos >= line->end)) { break; }
-@@ -686,7 +686,7 @@
- processIDS.clear();
- int exitCommand = 1;
-
--#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-+#if defined (__APPLE__) || (__MACH__) || (__unix__)
- int process = 1;
-
- //loop through and create all the processes you want
---- mothur-1.22.2.orig/uchime_src/myutils.cpp
-+++ mothur-1.22.2/uchime_src/myutils.cpp
-@@ -635,7 +635,7 @@
- g_PeakMemUseBytes = Bytes;
- return Bytes;
- }
--#elif linux || __linux__
-+#elif defined(__unix__)
- double GetMemUseBytes()
- {
- static char statm[64];
Modified: trunk/packages/mothur/trunk/debian/patches/makefile.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/makefile.patch 2012-03-08 14:38:55 UTC (rev 9957)
+++ trunk/packages/mothur/trunk/debian/patches/makefile.patch 2012-03-08 14:41:01 UTC (rev 9958)
@@ -1,8 +1,8 @@
Author: Steffen Moeller <moeller at debian.org>
Purpose: Comment MAC specific option
---- mothur-1.22.2.orig/makefile
-+++ mothur-1.22.2/makefile
-@@ -26,7 +26,7 @@
+--- mothur-1.23.1.orig/makefile
++++ mothur-1.23.1/makefile
+@@ -27,7 +27,7 @@
#CXX = g++44
#if you are a mac user use the following line
Modified: trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch 2012-03-08 14:38:55 UTC (rev 9957)
+++ trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch 2012-03-08 14:41:01 UTC (rev 9958)
@@ -1,9 +1,9 @@
Author: Andreas Tille <tille at debian.org>
Date: 2011-01-30
Dscription: There is no need to link against lncurses because its symbols are not used
---- mothur-1.22.2.orig/makefile
-+++ mothur-1.22.2/makefile
-@@ -59,8 +59,7 @@
+--- mothur-1.23.1.orig/makefile
++++ mothur-1.23.1/makefile
+@@ -60,8 +60,7 @@
ifeq ($(strip $(USEREADLINE)),yes)
CXXFLAGS += -DUSE_READLINE
LIBS = \
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