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Make build system semi-sane:
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* Respect CC, CXX, CFLAGS, CXXFLAGS, CPPFLAGS, LDFLAGS and LIBS
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* Remove default optimisation flags
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* Remove -fpermissive from DEFS (as source builds fine now)
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* Add large file support (LFS) via CPPFLAGS and not in Makefile
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--- a/makefile
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+++ b/makefile
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@@ -47,23 +47,20 @@
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#
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# compilation
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#
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-CXX= g++
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-KRCC= gcc
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-CC=gcc
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+CXX ?= g++
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+CC ?= gcc
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#
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#
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-CFLGS= -w -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -fpermissive -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -D_FILE_OFFSET_BITS=64 -DSAMTOOLS_AVAILABLE
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+DEFS = -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -DSAMTOOLS_AVAILABLE
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-OPT= -O
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#
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# Include directory for template classes must be included
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# in both compilation & link lines, even if .h file is
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# found in default path. C front, gotta love it.
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#
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-INC= -I/usr/X11R6/include -I/me1/gordon/samtools/samtools-0.1.18
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+INCLUDES = $(SAMTOOLS_CPPFLAGS)
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-DEPENDENCIES=
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#
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#
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# Linking
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@@ -80,12 +77,9 @@
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# /lib/ld-linux.so.2 (0x003ee000)
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#
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# To fix cut/paste bug, I've made X11 always dynamic.
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-CLIBS= -lX11
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-LPATH= -L/usr/X11R6/lib
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-ARCHIVES= /usr/X11R6/lib/libXm.a \
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-/usr/X11R6/lib/libXt.a /usr/X11R6/lib/libSM.a \
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-/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \
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-/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a
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+
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+MOTIF_LIBS ?= -lXm -lXt
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+ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS)
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@@ -94,7 +88,6 @@
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#
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#LDFLGS= -g
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# static linking
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-LDFLGS= -g -rdynamic
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#
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# the subdirectory used by cfront compilers gets cleaned
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@@ -112,10 +105,10 @@
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# general compilation rules for .cpp, .cxx, .c files
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#
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.cpp.o:
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- $(CXX) $(CFLGS) $(OPT) $(INC) -c $<
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $<
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.c.o:
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- $(CXX) $(CFLGS) $(OPT) $(INC) -c $<
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $<
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#
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# targets file included in generated makefile
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@@ -593,17 +586,23 @@
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writeToRewriteReferenceFile.o \
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xsynchronize.o
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+SUBDIRS := misc/454 misc/mktrace misc/phd2fasta
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+
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+all: consed $(SUBDIRS)
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+
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+$(SUBDIRS):
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+ $(MAKE) -C $@
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+
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+.PHONY: all $(SUBDIRS)
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+
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consed: $(CONSED_OBJS) makefile checkLicenseKeyStub.o
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- $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \
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- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS)
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+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS)
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trial_consed: $(CONSED_OBJS) makefile checkLicenseKey.o
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- $(CXX) $(INC) $(LDFLGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o \
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- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS)
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+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o $(ALL_LIBS)
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pure: $(CONSED_OBJS) makefile checkLicenseKeyStub.o
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- $(PURIFY) $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \
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- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS)
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+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS)
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clean:
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rm -rf *.o core $(TEMPLATE_DIR)
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@@ -613,15 +612,15 @@
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# the Solaris 5.x compiler cannot optimize the following
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consedResources.o:
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- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources.cpp
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consedResources2.o:
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- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources2.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources2.cpp
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# tlingit cannot optimize the following:
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guiEditResources.o:
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- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c guiEditResources.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c guiEditResources.cpp
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guiEditResources.o : \
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assemblyViewTagTypeAndLine.h assert.h bIsNumericDouble.h \
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--- a/misc/454/Makefile
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+++ b/misc/454/Makefile
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@@ -0,0 +1,16 @@
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+CC ?= cc
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+LIBM = -lm
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+
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+DEFS = -DANSI_C
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+
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+OBJS= sff2scf.c
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+
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+sff2scf: $(OBJS)
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+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM)
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+
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+.c.o:
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $<
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+
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+clean:
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+ rm -f $(OBJS) sff2scf
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+
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--- a/misc/mktrace/Makefile
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+++ b/misc/mktrace/Makefile
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@@ -1,13 +1,17 @@
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-CC= cc
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-CFLAGS= -g
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-CLIB= -lm
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+CC ?= cc
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+LIBM = -lm
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+
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+DEFS = -DANSI_C
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OBJS= mktrace.o readFASTA.o writeSCF.o synTrace.o \
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freeTrace.o rwUtil.o writePhd.o getTime.o \
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readQUAL.o
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mktrace: $(OBJS)
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- $(CC) $(CFLAGS) -o mktrace $(OBJS) $(CLIB)
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+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM)
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+
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+.c.o:
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $<
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clean:
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rm -f $(OBJS) mktrace
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--- a/misc/phd2fasta/Makefile
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+++ b/misc/phd2fasta/Makefile
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@@ -1,8 +1,9 @@
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-CC=cc
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-CFLAGS=-O -w
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-CLIB=-lm
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+CC ?= cc
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+LIBM = -lm
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-OBJ= phd2fasta.o \
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+DEFS = -DANSI_C
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+
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+OBJS= phd2fasta.o \
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readParam.o initParam.o checkParam.o \
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freeParam.o helpParam.o \
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readFOF.o readDIR.o readFOX.o \
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@@ -15,10 +16,11 @@
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INC= phd2fasta.h
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-SRC = $(OBJ:.o=.c)
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-
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-phd2fasta: $(OBJ)
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- $(CC) $(CFLAGS) -o phd2fasta $(OBJ) $(CLIB)
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+phd2fasta: $(OBJS)
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+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM)
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+
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+.c.o:
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $<
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clean:
|
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rm -f $(OBJ) phd2fasta
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