.gitignore

+# Compiled Object files
+*.o
+
+# Compiled Static libraries
+*.a
+
+# Executables
+src/long_seq_tm_test
+src/ntdpal
+src/ntthal
+src/oligotm
+src/primer3_core
+src/primer3_masker
+src/*.exe
+
+# Temporary Test Files
+test/primer1_list_tmp/*
+test/primer1_th_list_tmp/*
+test/primer_list_tmp/*
+test/th-w-other-tasks_list_tmp/*
+test/*.err
+test/*.tmp
+test/*.tmp2
+test/*.valg
+test/*.vg
+test/primer_global_err/*.tmp
+test/primer_global_err/*.tmp2
+test/primer_global_err/*.valg
+test/primer_global_err/*.vg
+
+# Individual Test Files
+test/hyb_probe_only.for
+test/hyb_probe_only.int
+test/left_only.for
+test/pcr_primers.for
+test/pcr_primers.rev
+test/pcr_primers_and_io.for
+test/pcr_primers_and_io.int
+test/pcr_primers_and_io.rev
+test/right_only.for
+test/right_only.rev
+test/syntax01.for
+test/syntax01.int
+test/syntax01.rev
+test/syntax02.for
+test/syntax02.int
+test/syntax02.rev
+test/syntax03.for
+test/syntax03.int
+test/syntax03.rev
+test/syntax04.for
+test/syntax04.int
+test/syntax04.rev
+test/syntax07.for
+test/syntax07.int
+test/syntax07.rev
+test/syntax09.for
+test/syntax09.int
+test/syntax09.rev
+test/syntax10.for
+test/syntax10.int
+test/syntax10.rev
+
+.DS_Store

README.md

+Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3").
+From mispriming libraries to sequence quality data to the generation of internal
+oligos, primer3 does it. C&perl.
+
+Installing
+----------
+
+`sudo apt-get install -y build-essential g++ cmake git-all`
+
+`git clone https://github.com/primer3-org/primer3.git primer3`
+
+`cd primer3/src`
+
+`make`
+
+`make test`
+
+
+Run Primer3
+-----------
+
+`./primer3_core ../example`
+
+
+Read the complete Primer3 manual
+--------------------------------
+[Primer3 Manual](http://primer3.org/primer3_manual.htm)
+
+or see /src/primer3_manual.htm

create_test_folders.pl

+#!/usr/bin/perl
+
+# ======================================================================
+# (c) Copyright 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008,2010,
+#  2011,2012,2016
+# Whitehead Institute for Biomedical Research, Steve Rozen, 
+# Andreas Untergasser and Helen Skaletsky
+# All rights reserved.
+# 
+#   This file is part of the primer3 suite.
+#
+#   The primer3 suite is free software; you can redistribute it and/or
+#   modify it under the terms of the GNU General Public License as
+#   published by the Free Software Foundation; either version 2 of the
+#   License, or (at your option) any later version.
+#
+#   This software is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this file (file gpl-2.0.txt in the source distribution); if
+#   not, write to the Free Software Foundation, Inc., 51 Franklin St,
+#   Fifth Floor, Boston, MA 02110-1301 USA
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# ======================================================================
+
+use warnings 'all';
+use strict;
+
+if (-d "test") {
+    if (-d "test/primer_list_tmp") {
+        print "Folder excists: test/primer_list_tmp\n";
+    } else {
+        mkdir "test/primer_list_tmp";
+        print "Created folder: test/primer_list_tmp\n";
+    }
+    if (-d "test/primer1_list_tmp") {
+        print "Folder excists: test/primer1_list_tmp\n";
+    } else {
+        mkdir "test/primer1_list_tmp";
+        print "Created folder: test/primer1_list_tmp\n";
+    }
+    if (-d "test/primer1_th_list_tmp") {
+        print "Folder excists: test/primer1_th_list_tmp\n";
+    } else {
+        mkdir "test/primer1_th_list_tmp";
+        print "Created folder: test/primer1_th_list_tmp\n";
+    }
+    if (-d "test/th-w-other-tasks_list_tmp") {
+        print "Folder excists: test/th-w-other-tasks_list_tmp\n";
+    } else {
+        mkdir "test/th-w-other-tasks_list_tmp";
+        print "Created folder: test/th-w-other-tasks_list_tmp\n";
+    }
+
+}
+else {
+    print "Run this script in the Primer3 root folder\n";
+}
+
+

debian/changelog

+primer3 (2.4.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Secure URI in watch file
+
+ -- Andreas Tille <tille@debian.org>  Wed, 21 Feb 2018 09:01:27 +0100
+
 primer3 (2.3.7-5) unstable; urgency=medium
 
   * d/upstream/metadata:

debian/watch

 version=4
-http://sf.net/primer3/primer3-[-src]*([\d.]*)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
+https://sf.net/primer3/primer3-[-src]*([\d.]*)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
 

example

 SEQUENCE_ID=example
-SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
-SEQUENCE_TARGET=37,21
-PRIMER_TASK=pick_detection_primers
+SEQUENCE_TEMPLATE=tattggtgaagcctcaggtagtgcagaatatgaaacttcaggatccagtgggcatgctactggtagtgctgccggccttacaggcattatggtggcaaagtcgacagagttta
+PRIMER_TASK=generic
 PRIMER_PICK_LEFT_PRIMER=1
-PRIMER_PICK_INTERNAL_OLIGO=1
+PRIMER_PICK_INTERNAL_OLIGO=0
 PRIMER_PICK_RIGHT_PRIMER=1
-PRIMER_OPT_SIZE=18
-PRIMER_MIN_SIZE=15
-PRIMER_MAX_SIZE=21
-PRIMER_MAX_NS_ACCEPTED=1
-PRIMER_PRODUCT_SIZE_RANGE=75-100
-P3_FILE_FLAG=1
-SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
+PRIMER_OPT_SIZE=20
+PRIMER_MIN_SIZE=18
+PRIMER_MAX_SIZE=22
+PRIMER_PRODUCT_SIZE_RANGE=75-150
 PRIMER_EXPLAIN_FLAG=1
 =

kmer_lists/readme.txt

+Currently, directory kmer_lists contains TEST files (because of the size of
+list files).
+
+To download kmer-lists or to make ones, please visit
+http://primer3.ut.ee/lists.htm or homepage of "FastGT package version
+4.0" at http://bioinfo.ut.ee/?page_id=167&lang=en
+
+By default Primer3 uses kmer-lists with k-mer size 11 and size 16. File name
+format should be for human homo_sapiens_11.list and homo_sapiens_16.list
+(species_name_wordlenght.list)
\ No newline at end of file

settings_files/p3_th_settings.txt

+Primer3 File - http://primer3.org
+P3_FILE_TYPE=settings
+
+PRIMER_FIRST_BASE_INDEX=1
+PRIMER_TASK=generic
+P3_FILE_ID=Settings for PCR amplification followed by Sanger sequencing on both strands using PCR primers
+# 2012 01 29
+PRIMER_MIN_THREE_PRIME_DISTANCE=3
+PRIMER_EXPLAIN_FLAG=1
+
+# Put something reasonable for PRIMER_MISPRIMING_LIBRARY depending
+# on the species you are designing primers for.
+PRIMER_MISPRIMING_LIBRARY=
+PRIMER_MAX_LIBRARY_MISPRIMING=12.00
+PRIMER_PAIR_MAX_LIBRARY_MISPRIMING=20.00
+
+PRIMER_PRODUCT_SIZE_RANGE=300-400 401-500 501-600 601-700 701-850 851-1001
+PRIMER_NUM_RETURN=5
+PRIMER_MAX_END_STABILITY=9.0
+#
+PRIMER_MAX_SELF_ANY_TH=45.00
+PRIMER_MAX_SELF_END_TH=35.00
+PRIMER_PAIR_MAX_COMPL_ANY_TH=45.00
+PRIMER_PAIR_MAX_COMPL_END_TH=35.00
+
+PRIMER_MAX_HAIRPIN_TH=24.00
+PRIMER_MAX_TEMPLATE_MISPRIMING_TH=40.00
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH=70.00
+PRIMER_MIN_SIZE=18
+PRIMER_OPT_SIZE=20
+PRIMER_MAX_SIZE=23
+PRIMER_MIN_TM=57.0
+PRIMER_OPT_TM=59.0
+PRIMER_MAX_TM=62.0
+PRIMER_PAIR_MAX_DIFF_TM=5.0
+
+# PRIMER_TM_FORMULA=1 means use the SantaLucia parameters (Proc Natl Acad Sci 95:1460-65)
+PRIMER_TM_FORMULA=1
+
+# PRIMER_SALT_CORRECTIONS=1 means used the salt correction in SantaLucia et al 1998
+PRIMER_SALT_CORRECTIONS=1
+
+PRIMER_SALT_MONOVALENT=50.0
+PRIMER_INTERNAL_SALT_MONOVALENT=50.0
+
+# Millimolar conc of MgCl+2
+PRIMER_SALT_DIVALENT=1.5
+PRIMER_INTERNAL_SALT_DIVALENT=1.5
+
+# Millimolar conc of dNTPs
+PRIMER_DNTP_CONC=0.6
+
+# Correct, 0, since we are assuming
+# no dNTP's present when hybridizing.
+PRIMER_INTERNAL_DNTP_CONC=0.0
+
+PRIMER_DNA_CONC=50.0
+PRIMER_INTERNAL_DNA_CONC=50.0
+
+PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT=1
+PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT=1
+PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/data/public/tools/primer3/primer3/trunk/src/primer3_config/
+PRIMER_LOWERCASE_MASKING=0
+#
+PRIMER_MIN_GC=30.0
+PRIMER_MAX_GC=70.0
+PRIMER_MAX_NS_ACCEPTED=0
+PRIMER_MAX_POLY_X=4
+PRIMER_OUTSIDE_PENALTY=0
+PRIMER_GC_CLAMP=0
+PRIMER_LIBERAL_BASE=1
+PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
+PRIMER_PICK_ANYWAY=1
+
+PRIMER_WT_TM_LT=1.0
+PRIMER_WT_TM_GT=1.0
+PRIMER_WT_SIZE_LT=1.0
+PRIMER_WT_SIZE_GT=1.0
+PRIMER_WT_GC_PERCENT_LT=0.0
+PRIMER_WT_GC_PERCENT_GT=0.0
+PRIMER_WT_SELF_ANY_TH=0.0
+PRIMER_WT_SELF_END_TH=0.0
+PRIMER_WT_HAIRPIN_TH=0.0
+PRIMER_WT_NUM_NS=0.0
+PRIMER_WT_LIBRARY_MISPRIMING=0.0
+PRIMER_WT_SEQ_QUAL=0.0
+PRIMER_WT_END_QUAL=0.0
+PRIMER_WT_POS_PENALTY=0.0
+PRIMER_WT_END_STABILITY=0.0
+PRIMER_WT_TEMPLATE_MISPRIMING_TH=0.0
+PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0.0
+PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0.0
+PRIMER_PAIR_WT_PRODUCT_TM_LT=0.0
+PRIMER_PAIR_WT_PRODUCT_TM_GT=0.0
+PRIMER_PAIR_WT_DIFF_TM=0.0
+PRIMER_PAIR_WT_COMPL_ANY_TH=0.0
+PRIMER_PAIR_WT_COMPL_END_TH=0.0
+PRIMER_PAIR_WT_LIBRARY_MISPRIMING=0.0
+PRIMER_PAIR_WT_PR_PENALTY=1.0
+PRIMER_PAIR_WT_IO_PENALTY=0.0
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=0.0
+=

primer3_v1_1_4_default_settings.txt → settings_files/primer3_v1_1_4_default_settings.txt

-Primer3 File - http://primer3.sourceforge.net
+Primer3 File - http://primer3.org
 P3_FILE_TYPE=settings
 
 P3_FILE_ID=Default settings of primer3 version 1.1.4

primer3web_v0_4_0_default_settings.txt → settings_files/primer3web_v0_4_0_default_settings.txt

-Primer3 File - http://primer3.sourceforge.net
+Primer3 File - http://primer3.org
 P3_FILE_TYPE=settings
 
 P3_FILE_ID=Default settings of primer3web version 0.4.0

primer3web_v3_0_0_default_settings.txt → settings_files/primer3web_v3_0_0_default_settings.txt

-Primer3 File - http://primer3.sourceforge.net
+Primer3 File - http://primer3.org
 P3_FILE_TYPE=settings
 
 PRIMER_FIRST_BASE_INDEX=1

primer3web_v4_0_0_default_settings.txt → settings_files/primer3web_v4_0_0_default_settings.txt

-Primer3 File - http://primer3.sourceforge.net
+Primer3 File - http://primer3.org
 P3_FILE_TYPE=settings
 
 PRIMER_FIRST_BASE_INDEX=1

src/Makefile

@@ -43,7 +43,7 @@
 # general users and for biologist programmers. In: Krawetz S, Misener S
 # (eds) Bioinformatics Methods and Protocols: Methods in Molecular
 # Biology. Humana Press, Totowa, NJ, pp 365-386.  Source code available
-# from https://sourceforge.net/projects/primer3/
+# from https://github.com/primer3-org/primer3
 # ======================================================================
 
 # For VALGRIND -- see end of this makefile for testing primer3_core
@@ -75,12 +75,14 @@ ifeq ($(TESTOPTS),--windows)
 	NTTHAL_EXE      = ntthal.exe
 	OLIGOTM_EXE     = oligotm.exe
 	LONG_SEQ_EXE	= long_seq_tm_test.exe
+	MASKER_EXE      = primer3_masker.exe
 else
 	PRIMER_EXE      = primer3_core
 	NTDPAL_EXE      = ntdpal
 	NTTHAL_EXE      = ntthal
 	OLIGOTM_EXE     = oligotm
 	LONG_SEQ_EXE	= long_seq_tm_test
+	MASKER_EXE      = primer3_masker
 endif
 LIBOLIGOTM      = liboligotm.a
 LIBOLIGOTM_DYN  = liboligotm.so.1.2.0
@@ -90,21 +92,24 @@ LIBTHAL         = libthal.a
 LIBTHAL_DYN     = libthal.a.so.1.0.0
 LIBPRIMER3      = libprimer3.a
 LIBPRIMER3_DYN  = libprimer3.so.1.0.0
-LIBRARIES       = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) 
-DYNLIBS         = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
+LIBMASKER       = libmasker.a
+LIBMASKER_DYN   = libmasker.a.so.1.0.0
+LIBRARIES       = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) $(LIBMASKER)
+DYNLIBS         = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN) $(LIBMASKER_DYN)
 RANLIB          = ranlib
 
 PRIMER_OBJECTS1=primer3_boulder_main.o\
                 format_output.o\
                 read_boulder.o\
-                print_boulder.o 
+                print_boulder.o\
+                masker.o
 
 PRIMER_OBJECTS=$(PRIMER_OBJECTS1) $(LIBRARIES)
 PRIMER_DYN_OBJECTS=$(PRIMER_OBJECTS1) $(DYNLIBS)
 # These are files generated by running ./primer3_core < ../example
 example_files=example.for example.rev example.int
 
-EXES=$(PRIMER_EXE) $(NTDPAL_EXE) $(NTTHAL_EXE) $(OLIGOTM_EXE) $(LONG_SEQ_EXE)
+EXES=$(PRIMER_EXE) $(NTDPAL_EXE) $(NTTHAL_EXE) $(OLIGOTM_EXE) $(LONG_SEQ_EXE) $(MASKER_EXE)
 
 all: $(EXES) $(LIBRARIES)
 
@@ -150,6 +155,13 @@ $(LIBPRIMER3): libprimer3.o p3_seq_lib.o
 $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
 	$(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
 
+$(LIBMASKER): masker.o
+	$(AR) rv $@ masker.o
+	$(RANLIB) $@
+               
+$(LIBMASKER_DYN): masker.o
+	$(CC) -shared -W1,-soname,libmasker.so.1 -o $(LIBMASKER_DYN) masker.o
+
 $(PRIMER_EXE): $(PRIMER_OBJECTS)
 	$(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
 
@@ -168,6 +180,9 @@ $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
 $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
 	$(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
 
+$(MASKER_EXE): masker_main.c $(LIBRARIES)
+	$(CPP) $(CFLAGS) -o $@ masker_main.c $(LIBRARIES) $(LIBOPTS) $(LDLIBS)
+
 read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h 
 	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
 
@@ -207,6 +222,9 @@ oligotm.o: oligotm.c oligotm.h
 primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h
 	$(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
 
+masker.o: masker.c masker.h libprimer3.h
+	$(CPP) -c $(CFLAGS) $(P_DEFINES) masker.c
+
 primer_test: test
 
 test: $(PRIMER_EXE) $(NTDPAL_EXE) $(NTTHAL_EXE)

src/Makefile.OSX

-# ======================================================================
-# (c) Copyright 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008,2009
-# Whitehead Institute for Biomedical Research, Steve Rozen,
-# Andreas Untergasser and Helen Skaletsky
-# All rights reserved.
-#
-#   This file is part of primer3, the libprimer3 library, the oligotm
-#   library and the dpal library.
-#
-#   Primer3 and the libraries above are free software; you can
-#   redistribute them and/or modify them under the terms of the GNU
-#   General Public License as published by the Free Software Foundation;
-#   either version 2 of the License, or (at your option) any later
-#   version.
-#
-#   This software is distributed in the hope that it will be useful,
-#   but WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#   GNU General Public License for more details.
-#
-#   You should have received a copy of the GNU General Public License
-#   along with this file (file gpl-2.0.txt in the source distribution); if
-#   not, write to the Free Software Foundation, Inc., 51 Franklin St,
-#   Fifth Floor, Boston, MA 02110-1301 USA
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-# OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-# ======================================================================
-
-# ======================================================================
-# CITING PRIMER3
-#
-# Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for
-# general users and for biologist programmers. In: Krawetz S, Misener S
-# (eds) Bioinformatics Methods and Protocols: Methods in Molecular
-# Biology. Humana Press, Totowa, NJ, pp 365-386.  Source code available
-# from https://sourceforge.net/projects/primer3/
-# ======================================================================
-
-# For VALGRIND -- see end of this makefile for testing primer3_core
-# with valgrind, a leak and memory access checker.
-TESTOPTS=
-WINMAKE=mingw32-make
-DEVELOPER=`xcode-select -print-path`
-
-# this is clumsy, but deals with the moving compilers on OSX
-
-ifndef SDKROOT
-	SDKROOT=$(DEVELOPER)/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk
-endif
-
-ifneq (exists, $(shell [ -d $(SDKROOT) ] && echo exists))
-	SDKROOT=$(DEVELOPER)/SDKs/MacOSX10.7.sdk
-endif
-
-ifndef MACOSX_DEPLOYMENT_TARGET
-	MACOSX_DEPLOYMENT_TARGET=10.6
-endif
-
-ifndef ARCHS
-	ARCHS=i386 x86_64
-endif
-
-LDLIBS     = -lm
-CC         = gcc
-CPP        = g++
-LIBTOOL    = libtool
-O_OPTS     = -O2
-CC_OPTS    = -g -Wall -D__USE_FIXED_PROTOTYPES__ -isysroot $(SDKROOT) -mmacosx-version-min=$(MACOSX_DEPLOYMENT_TARGET) $(foreach ARCH,$(ARCHS),-arch $(ARCH))
-P_DEFINES  =
-
-CFLAGS  = $(CC_OPTS) $(O_OPTS)
-LDFLAGS = -g $(foreach ARCH,$(ARCHS),-arch $(ARCH))
-
-# ======================================================================
-# If you have trouble with library skew when moving primer3 executables
-# between systems, you might want to set LIBOPTS to -static
-LIBOPTS =
-
-ifeq ($(TESTOPTS),--windows)
-	PRIMER_EXE      = primer3_core.exe
-	NTDPAL_EXE	= ntdpal.exe
-	NTTHAL_EXE	= ntthal.exe
-	OLIGOTM_EXE	= oligotm.exe
-	LONG_SEQ_EXE	= long_seq_tm_test.exe
-else
-	PRIMER_EXE      = primer3_core
-	NTDPAL_EXE	= ntdpal
-	NTTHAL_EXE	= ntthal
-	OLIGOTM_EXE	= oligotm
-	LONG_SEQ_EXE	= long_seq_tm_test
-endif
-LIBOLIGOTM      = liboligotm.a
-LIBOLIGOTM_DYN  = liboligotm.so.1.2.0
-LIBDPAL         = libdpal.a
-LIBDPAL_DYN     = libdpal.a.so.1.0.0
-LIBTHAL         = libthal.a
-LIBTHAL_DYN     = libthal.a.so.1.0.0
-LIBPRIMER3      = libprimer3.a
-LIBPRIMER3_DYN  = libprimer3.so.1.0.0
-LIBRARIES       = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM)
-DYNLIBS         = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
-
-PRIMER_OBJECTS1=primer3_boulder_main.o\
-                format_output.o\
-                read_boulder.o\
-                print_boulder.o
-
-PRIMER_OBJECTS=$(PRIMER_OBJECTS1) $(LIBRARIES)
-PRIMER_DYN_OBJECTS=$(PRIMER_OBJECTS1) $(DYNLIBS)
-# These are files generated by running ./primer3_core < ../example
-example_files=example.for example.rev example.int
-
-EXES=$(PRIMER_EXE) $(NTDPAL_EXE) $(NTTHAL_EXE) $(OLIGOTM_EXE) $(LONG_SEQ_EXE)
-
-all: $(EXES) $(LIBRARIES)
-
-clean_src:
-ifeq ($(TESTOPTS),--windows)
-	del /Q /F *.o $(EXES) *~ $(LIBRARIES) $(example_files) core ..\*~
-else
-	-rm -f *.o $(EXES) *~ $(LIBRARIES) $(DYNLIBS) $(example_files) core ../*~
-endif
-
-clean: clean_src
-ifeq ($(TESTOPTS),--windows)
-	cd ..\test & $(WINMAKE) clean TESTOPTS=$(TESTOPTS)
-else
-	cd ../test/; make clean
-endif
-
-$(LIBOLIGOTM): oligotm.o
-	$(LIBTOOL) -static -o $@ oligotm.o
-
-$(LIBOLIGOTM_LIB): oligotm.o
-	$(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
-
-$(LIBDPAL): dpal_primer.o
-	$(LIBTOOL) -static -o $@ dpal_primer.o
-
-$(LIBDPAL_DYN): dpal_primer.o
-	$(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
-
-$(LIBTHAL): thal_primer.o
-	$(LIBTOOL) -static -o $@ thal_primer.o
-
-$(LIBTHAL_DYN): thal_primer.o
-	$(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
-
-$(LIBPRIMER3): libprimer3.o p3_seq_lib.o
-	$(LIBTOOL) -static -o $@ libprimer3.o p3_seq_lib.o
-
-$(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
-	$(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
-
-$(PRIMER_EXE): $(PRIMER_OBJECTS)
-	$(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
-
-libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h
-	$(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
-
-$(NTDPAL_EXE): ntdpal_main.o dpal.o
-	$(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
-
-$(NTTHAL_EXE): thal_main.o thal.o
-	$(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
-
-$(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
-	$(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
-
-$(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
-	$(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
-
-read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h
-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
-
-print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h
-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c
-
-dpal.o: dpal.c dpal.h
-	$(CPP) -c $(CFLAGS) -o $@ dpal.c
-
-# We use '-ffloat-store' on windows to prevent undesirable
-# precision which may lead to differences in floating point results.
-thal.o: thal.c thal.h
-	$(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c
-
-p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
-	$(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c
-
-dpal_primer.o: dpal.c dpal.h
-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
-
-thal_primer.o: thal.c thal.h
-	$(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
-
-format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h
-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
-
-ntdpal_main.o: ntdpal_main.c dpal.h
-	$(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c
-
-thal_main.o: thal_main.c thal.h
-	$(CPP) -c $(CFLAGS) -o $@ thal_main.c
-# We use CC_OPTS above rather than CFLAGS because
-# gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
-
-oligotm.o: oligotm.c oligotm.h
-
-primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h
-	$(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
-
-primer_test: test
-
-test: $(PRIMER_EXE) $(NTDPAL_EXE) $(NTTHAL_EXE)
-ifeq ($(TESTOPTS),--windows)
-	cd ..\test & $(WINMAKE) TESTOPTS=$(TESTOPTS)
-else
-	cd ../test; make test
-endif
-
-# ======================================================================
-#
-# VALGRIND INSTRUCTIONS.
-#
-# These instructions work for linux, and run the 'memcheck'
-# functionality of valgrind.  Tests will be _much_ slower
-# when running with valgrind checks.
-#
-# If necessary, get and install valgrind (should come with most
-# Linux's, but you need valgrind >= 3.2.3)
-#
-# In the src directory for primer3:
-#
-# $ make clean
-#
-# Re-complile without optimization and run the normal tests, does
-# _not_ valgrind them:
-#
-# $ make O_OPTS=-O0 test  # The value of O_OPTS is Minus Oh Zero
-#
-# Run valgrind on a small example:
-#
-# $ valgrind --leak-check=yes --show-reachable=yes --log-file-exactly=p3vg ./primer3_core < ../example
-#
-# Check output in file p3vg
-#
-# Note: Valgrind is at /usr/local/bin/valgrind at WI
-#
-# OK, now for the real tests:
-#
-# $ cd ../test
-#
-# Check valgrind path in p3test.pl, ntdpal_test.pl, and oligotm_test.pl
-# and correct if necessary.  This code works under valgrind 3.2.3.
-#
-# $ make TESTOPTS=--valgrind  # Remember, you have to be in test/
-#
-# When the --valgrind flag is set, the perl test scripts grep for and
-# display errors and leaks, but you need to ***look at the output** to
-# see these and figure out which test caused the problem, so you can
-# debug it.
-#
-# ======================================================================