[Makefile] Use user's CPPFLAGS/LDFLAGS/LIBS variables

Use these variables in relevant compilation and linking rules so they can
be overridden by the user in the usual autoconf-style way.  Fixes samtools#222.

Remove DFLAGS and INCLUDES, using the conventional CPPFLAGS instead.
Add EXTRA_CPPFLAGS in their place, for our own various options that
need to stay set even if the user overrides CPPFLAGS.  If we end up
with necessary compiler or linker options or libraries, we'll add
EXTRA_CFLAGS, EXTRA_LDFLAGS, or EXTRA_LIBS accordingly.

Rename *_LDLIBS to *_LIBS; it seems that LDLIBS doesn't particularly
exist outside GNU Make's built-in rules.  Instead LIBS is configure's
conventional variable for the purpose, so is the right thing to use
for a user-visible variable.

Makefile

@@ -36,23 +36,28 @@ BGZIP  = $(HTSDIR)/bgzip
 TABIX  = $(HTSDIR)/tabix
 
 CC       = gcc
+CPPFLAGS =
 CFLAGS   = -g -Wall -Wc++-compat -O2
-DFLAGS   =
+LDFLAGS  =
+LIBS     =
+
 OBJS     = main.o vcfindex.o tabix.o \
            vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
            vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o \
            vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
            vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
            ccall.o em.o prob1.o kmin.o # the original samtools calling
-INCLUDES = -I. -I$(HTSDIR)
+
+EXTRA_CPPFLAGS = -I. -I$(HTSDIR)
+GSL_LIBS       =
 
 # The polysomy command is not compiled by default because it brings dependency
 # on libgsl. The command can be compiled wth `make USE_GPL=1`. See the INSTALL
 # and LICENSE documents to understand license implications.
 ifdef USE_GPL
-    CFLAGS += -DUSE_GPL
-    OBJS   += polysomy.o
-    LDLIBS  = -lgsl -lcblas
+    EXTRA_CPPFLAGS += -DUSE_GPL
+    OBJS += polysomy.o
+    GSL_LIBS = -lgsl -lcblas
 endif
 
 prefix      = /usr/local
@@ -88,7 +93,7 @@ version.h:
 force:
 
 .c.o:
-	$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+	$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $<
 
 test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
 	./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
@@ -103,7 +108,7 @@ PLUGINS = $(PLUGINC:.c=.so)
 PLUGINM = $(PLUGINC:.c=.mk)
 
 %.so: %.c version.h version.c $(HTSDIR)/libhts.so
-	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts
+	$(CC) -fPIC -shared $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -L$(HTSDIR) $(LDFLAGS) -o $@ version.c $< -lhts $(LIBS)
 
 -include $(PLUGINM)
 
@@ -156,10 +161,10 @@ version.o: version.h version.c
 test/test-rbuf.o: test/test-rbuf.c rbuf.h
 
 test/test-rbuf: test/test-rbuf.o
-	$(CC) $(CFLAGS) -o $@ -lm -ldl $<
+	$(CC) $(LDFLAGS) -o $@ $^ -lm -ldl $(LIBS)
 
 bcftools: $(HTSLIB) $(OBJS)
-	$(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
+	$(CC) $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
 
 doc/bcftools.1: doc/bcftools.txt
 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt

plugins/fixploidy.mk

@@ -1,2 +1,2 @@
 plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
-	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
+	$(CC) -fPIC -shared $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -L$(HTSDIR) $(LDFLAGS) -o $@ ploidy.c version.c $< -lhts $(LIBS)

plugins/vcf2sex.mk

@@ -1,2 +1,2 @@
 plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
-	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
+	$(CC) -fPIC -shared $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -L$(HTSDIR) $(LDFLAGS) -o $@ ploidy.c version.c $< -lhts $(LIBS)