Merge pull request #11 from iainrb/devel

Changes for release 1.6

Author: jenniferliddle

.gitignore

@@ -14,3 +14,19 @@
 *.lai
 *.la
 *.a
+
+# Temporary test directories
+temp*
+
+# Files generated by cxxtest
+test_simtools.cpp
+runner
+runner.cpp
+
+# Compiled executables
+sim
+simtools
+g2i
+gtc
+gtc_process
+normalize_manifest

Gtc.cpp

@@ -9,26 +9,27 @@
 //
 // Author: Jennifer Liddle <js10@sanger.ac.uk, jennifer@jsquared.co.uk>
 //
-// Redistribution and use in source and binary forms, with or without modification, 
-// are permitted provided that the following conditions are met:
-// 1. Redistributions of source code must retain the above copyright notice, this 
-// list of conditions and the following disclaimer.
-// 2. Redistributions in binary form must reproduce the above copyright notice, 
-// this list of conditions and the following disclaimer in the documentation and/or 
-// other materials provided with the distribution.
-// 3. Neither the name of the Genome Research Ltd nor the names of its contributors 
-// may be used to endorse or promote products derived from software without specific 
-// prior written permission.
+// Redistribution and use in source and binary forms, with or without 
+// modification, are permitted provided that the following conditions are met:
+// 1. Redistributions of source code must retain the above copyright notice, 
+// this list of conditions and the following disclaimer.
+// 2. Redistributions in binary form must reproduce the above copyright 
+// notice, this list of conditions and the following disclaimer in the 
+// documentation and/or other materials provided with the distribution.
+// 3. Neither the name of Genome Research Ltd nor the names of the 
+// contributors may be used to endorse or promote products derived from 
+// software without specific prior written permission.
 //
-// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR WARRANTIES, 
-// INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 
-// FOR A PARTICULAR PURPOSE ARE DISCLAIMED. EVENT SHALL GENOME RESEARCH LTD. BE LIABLE 
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
-// (INCLUDING, 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.
+// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 GENOME RESEARCH LTD. 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.
 //
 //
 #include "Gtc.h"

Gtc.h

@@ -10,26 +10,29 @@
 
 // Author: Jennifer Liddle <js10@sanger.ac.uk, jennifer@jsquared.co.uk>
 //
-// Redistribution and use in source and binary forms, with or without modification, 
-// are permitted provided that the following conditions are met:
-// 1. Redistributions of source code must retain the above copyright notice, this
-// list of conditions and the following disclaimer.
-// 2. Redistributions in binary form must reproduce the above copyright notice, 
-// this list of conditions and the following disclaimer in the documentation and/or
-// other materials provided with the distribution.
-// 3. Neither the name of the Genome Research Ltd nor the names of its contributors 
-// may be used to endorse or promote products derived from software without specific
-// prior written permission.
 //
-// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR WARRANTIES, 
-// INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 
-// FOR A PARTICULAR PURPOSE ARE DISCLAIMED. EVENT SHALL GENOME RESEARCH LTD. BE LIABLE 
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
-// (INCLUDING, 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.
+// Redistribution and use in source and binary forms, with or without 
+// modification, are permitted provided that the following conditions are met:
+// 1. Redistributions of source code must retain the above copyright notice, 
+// this list of conditions and the following disclaimer.
+// 2. Redistributions in binary form must reproduce the above copyright 
+// notice, this list of conditions and the following disclaimer in the 
+// documentation and/or other materials provided with the distribution.
+// 3. Neither the name of Genome Research Ltd nor the names of the 
+// contributors may be used to endorse or promote products derived from 
+// software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 GENOME RESEARCH LTD. 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.
+//
 //
 
 #ifndef _GTC_H

Makefile

@@ -8,67 +8,90 @@
 
 # Author: Jennifer Liddle <js10@sanger.ac.uk, jennifer@jsquared.co.uk>
 #
-# Redistribution and use in source and binary forms, with or without modification, 
-# are permitted provided that the following conditions are met:
-# 1. Redistributions of source code must retain the above copyright notice, this
-# list of conditions and the following disclaimer.
-# 2. Redistributions in binary form must reproduce the above copyright notice, 
-# this list of conditions and the following disclaimer in the documentation and/or
-# other materials provided with the distribution.
-# 3. Neither the name of the Genome Research Ltd nor the names of its contributors 
-# may be used to endorse or promote products derived from software without specific
-# prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR WARRANTIES, 
-# INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 
-# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. EVENT SHALL GENOME RESEARCH LTD. BE LIABLE 
-# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
-# (INCLUDING, 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.
-#
 
-INSTALLLIB=/software/varinf/lib
+# Redistribution and use in source and binary forms, with or without 
+# modification, are permitted provided that the following conditions are met:
+# 1. Redistributions of source code must retain the above copyright notice, 
+# this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright 
+# notice, this list of conditions and the following disclaimer in the 
+# documentation and/or other materials provided with the distribution.
+# 3. Neither the name of Genome Research Ltd nor the names of the 
+# contributors may be used to endorse or promote products derived from 
+# software without specific prior written permission.
+
+# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 GENOME RESEARCH LTD. 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.
+
+
+
+.PHONY: test # always run, regardless of timestamps
+
+DIR = INSTALL_DIRECTORY # placeholder for main installation directory
+BIN=$(DIR)/bin
+# default directories for g2i 
+INSTALLLIB=/software/varinf/lib 
 INSTALLBIN=/software/varinf/bin
+# other useful paths
 STLPORT_INC=/software/solexa/pkg/STLport/current/stlport
 STLPORT_LIB=/software/solexa/pkg/STLport/current/build/lib/obj/gcc/so
 #STLPORT_INC=/software/varinf/lib/STLport/include/stlport
 #STLPORT_LIB=/software/varinf/lib/STLport/lib
 PERL_CORE=/usr/lib/perl/5.8.8/CORE
 PERL_CORE=/software/perl-5.8.8/lib/5.8.8/x86_64-linux-thread-multi/CORE
 
-TARGETS=libplinkbin.so gtc g2i b2i b2g gtc_process sim simtools
+
+TARGETS=libplinkbin.so gtc g2i gtc_process sim simtools normalize_manifest
 PERL_TARGETS=Gtc.so Sim.so
 LIBS=Gtc.o win2unix.o Sim.o
 
 # To compile with debug information added, invoke as (say): 
 # make DEBUG='y'
 # to build all targets with debug info. 
 # For just one target, say:
-# make DEBUG='y' b2i
+# make DEBUG='y' simtools
 
 CC=/usr/bin/g++
 
 # do NOT use -ffast-math, as it causes errors in infinity/NaN handling
 ifeq ($(DEBUG),y)
-	CFLAGS=-g -Wall -fPIC -O0 -I$(STLPORT_INC)
+	CFLAGS=-g -Wall -fPIC -O0 -I$(STLPORT_INC) -std=c++0x
 else
-	CFLAGS=-Wall -fPIC -O3 -I$(STLPORT_INC)
+	CFLAGS=-Wall -fPIC -O3 -I$(STLPORT_INC) -std=c++0x
 endif
 # Set runpath instead of relying on LD_LIBRARY_PATH
-LDFLAGS=-Wl,-rpath -Wl,$(STLPORT_LIB) -L$(STLPORT_LIB) -lstlport -lm
+LDFLAGS=-Wl,-rpath -Wl,$(STLPORT_LIB) -L$(STLPORT_LIB) -lstlport -lm 
+CXXFLAGS=-Wno-deprecated -I/software/gapi/pkg/cxxtest/4.2.1/
+
+usage:
+	@echo -e "Usage: make install DIR=<destination directory>\nOther targets: make all, make test, make install_g2i"
 
-default: all
 
 clean:
-	rm -f *.o Gtc_wrap.cxx Gtc.pm Sim_wrap.cxx Sim.pm $(TARGETS)
+	rm -f *.o Gtc_wrap.cxx Gtc.pm Sim_wrap.cxx Sim.pm runner.cpp runner $(TARGETS)
+
+test: Sim.o Gtc.o Manifest.o QC.o json/json_reader.o json/json_writer.o json/json_value.o commands.o runner.o
+	$(CC) $(CFLAGS) $(LDFLAGS) $(CXXFLAGS) -o runner $^ -lstlport
+	./runner # run "./runner -v" to print trace information
 
-test:
-	run_tests
+runner.o: all
+	cxxtestgen --error-printer -o runner.cpp test_simtools.h
+	$(CC) -c $(CFLAGS) $(LDFLAGS) $(CXXFLAGS)  -o $@ runner.cpp
 
 install: all
+	install -d $(BIN) 
+	install g2i gtc normalize_manifest sim simtools $(BIN)
+	@echo -e "Simtools successfully installed."
+
+install_g2i: all
 	cp Gtc.pm $(INSTALLLIB)
 	cp Gtc.so $(INSTALLLIB)
 	cp Sim.pm $(INSTALLLIB)
@@ -82,24 +105,24 @@ perl: $(PERL_TARGETS)
 gtc: gtc.o Gtc.o Manifest.o
 	$(CC) $(LDFLAGS) -o $@ $^ -lstlport
 
+normalize_manifest: normalize_manifest.o Manifest.o
+	$(CC) $(LDFLAGS) -o $@ $^ -lstlport
+
 sim: sim.o Sim.o
 	$(CC) $(LDFLAGS) -o $@ $^ -lstlport
 
-simtools: simtools.o Sim.o Gtc.o Manifest.o QC.o json/json_reader.o json/json_writer.o json/json_value.o
+simtools: simtools.o commands.o Sim.o Gtc.o Manifest.o QC.o json/json_reader.o json/json_writer.o json/json_value.o
 	$(CC) $(LDFLAGS) -o $@ $^ -lstlport
 
+commands.o: commands.cpp
+	$(CC) -c  $(CFLAGS) $(CPPFLAGS) -o $@ $<
+
 manifest: manifest.o Manifest.o
 	$(CC) $(LDFLAGS) -o $@ $^ -lstlport
 
 g2i: g2i.o Gtc.o Manifest.o win2unix.o Sim.o json/json_reader.o json/json_writer.o json/json_value.o utilities.o plink_binary.o
 	$(CC) $(LDFLAGS) -o $@ $^ -lstlport
 
-b2i: b2i.o Manifest.o b2base.o             # "b2" code needs ssl library;
-	$(CC) $(LDFLAGS) -lssl  -o $@ $^ -lstlport -lssl       # pick this up from /usr/lib
-
-b2g: b2g.o Manifest.o b2base.o
-	$(CC) $(LDFLAGS) -lssl -o $@ $^ -lstlport -lssl      # Ditto.
-
 gtc_process: Gtc.o Manifest.o gtc_process.o 
 	$(CC) $(LDFLAGS) -o $@ $^ -lstlport
 
@@ -132,9 +155,6 @@ gtc.o: Gtc.h Manifest.h
 sim.o: Sim.h
 simtools.o: Sim.h
 g2i.o: Gtc.h Manifest.h plink_binary.h
-b2base.o: b2base.cpp
-b2i.o: b2i.cpp Manifest.h
-b2g.o: b2g.cpp Manifest.h
 win2unix.o: win2unix.cpp win2unix.h
 plink_binary.o: plink_binary.cpp plink_binary.h