--- Makefile.orig	2017-03-14 07:26:49.191430557 +0100
+++ Makefile	2017-03-14 07:27:44.929678345 +0100
@@ -29,20 +29,10 @@
 all: $(PROG) $(TEST_PROG)
 
 # Adjust $(HTSDIR) to point to your top-level htslib directory
-HTSDIR = htslib-1.4.1
-include $(HTSDIR)/htslib.mk
-include $(HTSDIR)/htslib_static.mk
-HTSLIB = $(HTSDIR)/libhts.a
-BGZIP  = $(HTSDIR)/bgzip
-TABIX  = $(HTSDIR)/tabix
-HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
-HTSLIB_LIBS = $(HTSLIB_static_LIBS)
+HTSDIR = /usr/include
 
 CC       = gcc
-CPPFLAGS =
-CFLAGS   = -g -Wall -Wc++-compat -O2
-LDFLAGS  =
-LIBS     =
+CFLAGS   := -g -Wall -Wc++-compat -O2 $(CFLAGS)
 
 ifeq "$(shell uname -s)" "Darwin"
 DYNAMIC_FLAGS = -Wl,-export_dynamic
@@ -51,8 +41,8 @@
 endif
 
 # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
-ALL_LDFLAGS  = $(DYNAMIC_FLAGS) $(HTSLIB_LDFLAGS) $(LDFLAGS)
+ALL_CPPFLAGS = -I. $(CPPFLAGS)
+ALL_LDFLAGS  = $(DYNAMIC_FLAGS) $(LDFLAGS)
 ALL_LIBS     = -lm -lz -ldl $(LIBS)
 
 OBJS     = main.o vcfindex.o tabix.o \
@@ -64,7 +54,7 @@
            mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
            ccall.o em.o prob1.o kmin.o # the original samtools calling
 
-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
+EXTRA_CPPFLAGS = -I. -DPLUGINPATH=\"$(pluginpath)\"
 GSL_LIBS       =
 
 # The polysomy command is not compiled by default because it brings dependency
@@ -73,7 +63,7 @@
 ifdef USE_GPL
     EXTRA_CPPFLAGS += -DUSE_GPL
     OBJS += polysomy.o peakfit.o
-    GSL_LIBS = -lgsl -lcblas
+    GSL_LIBS = -lgsl -lgslcblas
 endif
 
 prefix      = /usr/local
@@ -117,12 +107,12 @@
 .c.o:
 	$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
 
-test: $(PROG) plugins test/test-rbuf test/test-regidx $(BGZIP) $(TABIX)
+test: $(PROG) plugins test/test-rbuf test/test-regidx
 	./test/test-regidx
-	./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
+	./test/test.pl --exec bgzip=bgzip --exec tabix=tabix
 
-test-plugins: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
-	./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
+test-plugins: $(PROG) plugins test/test-rbuf
+	./test/test.pl --plugins --exec bgzip=bgzip --exec tabix=tabix
 
 
 # Plugin rules
@@ -208,11 +198,11 @@
 
 test/test-regidx.o: test/test-regidx.c regidx.h
 
-test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS)
+test/test-regidx: test/test-regidx.o regidx.o
+	$(CC) $(ALL_LDFLAGS) -o $@ $^ -lpthread -lhts $(ALL_LIBS)
 
-bcftools: $(HTSLIB) $(OBJS)
-	$(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
+bcftools: $(OBJS)
+	$(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) -lpthread -lhts $(GSL_LIBS) $(ALL_LIBS)
 
 doc/bcftools.1: doc/bcftools.txt
 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt