--- a/config.mk.in
+++ b/config.mk.in
@@ -28,27 +28,26 @@
 # in the Makefile to reflect your configuration choices.  If you don't run
 # configure, the main Makefile contains suitable conservative defaults.
 
-prefix       = @prefix@
-exec_prefix  = @exec_prefix@
-bindir       = @bindir@
-datarootdir  = @datarootdir@
-mandir       = @mandir@
+prefix      = @prefix@
+exec_prefix = @exec_prefix@
+bindir      = @bindir@
+libdir      = @libdir@
+datarootdir = @datarootdir@
+mandir      = @mandir@
+man1dir     = $(mandir)/man1
 
 CC       = @CC@
+AR       = @AR@
 CPPFLAGS = @CPPFLAGS@
 CFLAGS   = @CFLAGS@
 LDFLAGS  = @LDFLAGS@
 LIBS     = @LIBS@
 
-@Hsource@HTSDIR = @HTSDIR@
-@Hsource@include $(HTSDIR)/htslib.mk
-@Hsource@include $(HTSDIR)/htslib_static.mk
-@Hsource@HTSLIB = $(HTSDIR)/libhts.a
-@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
-@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
-@Hsource@BGZIP = $(HTSDIR)/bgzip
-HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
-@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
-@Hinstall@HTSLIB_LIB = -lhts
+HTSLIB_CFLAGS = @HTSLIB_CFLAGS@
+HTSLIB_LIBS = @HTSLIB_LIBS@
 
-CURSES_LIB = @CURSES_LIB@
+NCURSES_CFLAGS = @NCURSES_CFLAGS@
+NCURSES_LIBS = @NCURSES_LIBS@
+
+ZLIB_CFLAGS = @ZLIB_CFLAGS@
+ZLIB_LIBS = @ZLIB_LIBS@
--- a/configure.ac
+++ b/configure.ac
@@ -29,9 +29,6 @@
 AC_CONFIG_SRCDIR([bamtk.c])
 AC_CONFIG_HEADERS([config.h])
 
-m4_include([m4/ax_with_curses.m4])
-m4_include([m4/ax_with_htslib.m4])
-
 dnl Copyright notice to be copied into the generated configure script
 AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
 
@@ -39,73 +36,27 @@
 redistribute it.  There is NO WARRANTY, to the extent permitted by law.])
 
 AC_PROG_CC
+AM_PROG_AR
 
 AC_SYS_LARGEFILE
 
-AX_WITH_HTSLIB
-if test "$ax_cv_htslib" != yes; then
-  AC_MSG_ERROR([HTSlib development files not found
-
-Samtools uses HTSlib to parse bioinformatics file formats etc.  Building it
-requires an unpacked HTSlib source tree (which will be built in conjunction
-with samtools) or a previously-installed HTSlib.  In either case you may
-need to configure --with-htslib=DIR to locate the appropriate HTSlib.
-
-FAILED.  You must supply an HTSlib in order to build samtools successfully.])
-fi
-
-if test "$ax_cv_htslib_which" = source; then
-  Hsource=
-  Hinstall='#'
-else
-  Hsource='#'
-  Hinstall=
-fi
-AC_SUBST([Hsource])
-AC_SUBST([Hinstall])
+dnl htslib
+PKG_CHECK_MODULES([HTSLIB], [htslib])
 
+dnl ncurses
 AC_ARG_WITH([curses],
   [AS_HELP_STRING([--without-curses],
                   [omit curses support, so no curses library needed])])
 
-if test "$with_curses" != no; then
-  AX_WITH_CURSES
-  if test "$ax_cv_curses" != yes; then
-    AC_MSG_ERROR([curses development files not found
-
-The 'samtools tview' command uses the curses text user interface library.
-Building samtools with tview requires curses/ncurses/etc development files
-to be installed on the build machine; you may need to ensure a package such
-as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based
-Linux distributions) is installed.
-
-FAILED.  Either configure --without-curses or resolve this error to build
-samtools successfully.])
-  fi
-else
-  CURSES_LIB=
-  CURSES_CPPFLAGS=
-  AC_SUBST([CURSES_LIB])
-  AC_SUBST([CURSES_CPPFLAGS])
-fi
-
-save_LIBS=$LIBS
-zlib_devel=ok
-dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests
-AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;])
-AC_CHECK_LIB(z, inflate,  [], [zlib_devel=missing])
-LIBS=$save_LIBS
-
-if test $zlib_devel != ok; then
-  AC_MSG_ERROR([zlib development files not found
-
-Samtools uses compression routines from the zlib library <http://zlib.net>.
-Building samtools requires zlib development files to be installed on the build
-machine; you may need to ensure a package such as zlib1g-dev (on Debian or
-Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed.
+AS_IF([test "x$with_curses" != "xno"], [
+  PKG_CHECK_MODULES([NCURSES], [ncurses])
+
+  AC_DEFINE([HAVE_CURSES], [1])
+  AC_DEFINE([HAVE_NCURSES_H], [1])
+])
 
-FAILED.  This error must be resolved in order to build samtools successfully.])
-fi
+dnl zlib
+PKG_CHECK_MODULES([ZLIB], [zlib])
 
 AC_CONFIG_FILES([config.mk])
 AC_OUTPUT
--- a/Makefile
+++ b/Makefile
@@ -21,14 +21,6 @@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC       = gcc
-AR       = ar
-CPPFLAGS =
-#CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
-CFLAGS   = -g -Wall -O2
-LDFLAGS  =
-LIBS     =
-
 LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
             sam_header.o bam_plbuf.o
 AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
@@ -40,13 +32,6 @@
             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
             bam_quickcheck.o bam_addrprg.o
 
-prefix      = /usr/local
-exec_prefix = $(prefix)
-bindir      = $(exec_prefix)/bin
-datarootdir = $(prefix)/share
-mandir      = $(datarootdir)/man
-man1dir     = $(mandir)/man1
-
 # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
 misc_bindir = $(bindir)
 
@@ -85,15 +70,14 @@
 
 all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS)
 
-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
-ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)
-ALL_LIBS     = -lz $(LIBS)
+ALL_CPPFLAGS = -I. $(HTSLIB_CFLAGS) $(CPPFLAGS)
+ALL_LIBS     = $(ZLIB_LIBS) $(LIBS)
 
 # Usually config.mk and config.h are generated by running configure
 # or config.status, but if those aren't used create defaults here.
 
 config.mk:
-	@sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@
+	@sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CFLAGS@/-I$$(HTSDIR)/g;s/@NCURSES_LIBS@/-lcurses/g' config.mk.in > $@
 
 config.h:
 	echo '/* Basic config.h generated by Makefile */' > $@
@@ -133,17 +117,22 @@
 .c.o:
 	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
 
+$(LOBJS):
+	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -fPIC -c -o $@ $<
+
 
 LIBST_OBJS = sam_opts.o sam_utils.o
 
 
-lib:libbam.a
+lib: libbam.so.1.0
 
-libbam.a:$(LOBJS)
-	$(AR) -csru $@ $(LOBJS)
+libbam.so.1.0:$(LOBJS)
+	$(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB)
+	ln -sf $@ libbam.so.1
+	ln -sf $@ libbam.so
 
-samtools: $(AOBJS) libbam.a libst.a $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread
+samtools: $(AOBJS) libbam.so.1.0 libst.a
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.so.1.0 libst.a $(HTSLIB_LIBS) $(NCURSES_LIBS) -lm $(ALL_LIBS) -lpthread
 
 # For building samtools and its test suite only: NOT to be installed.
 libst.a: $(LIBST_OBJS)
@@ -151,58 +140,58 @@
 	$(AR) -rcs $@ $(LIBST_OBJS)
 
 
-bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
-bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h)
-bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
-bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h)
-sam_h = sam.h $(htslib_sam_h) $(bam_h)
-sam_opts_h = sam_opts.h $(htslib_hts_h)
-sample_h = sample.h $(htslib_kstring_h)
-
-bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h
-bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h)
-bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h)
-bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h)
-bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h)
+bam_h = bam.h
+bam2bcf_h = bam2bcf.h
+bam_lpileup_h = bam_lpileup.h
+bam_plbuf_h = bam_plbuf.h
+bam_tview_h = bam_tview.h $(bam2bcf_h) $(bam_lpileup_h)
+sam_h = sam.h $(bam_h)
+sam_opts_h = sam_opts.h
+sample_h = sample.h
+
+bam.o: bam.c config.h $(bam_h) sam_header.h
+bam2bcf.o: bam2bcf.c config.h $(bam2bcf_h)
+bam2bcf_indel.o: bam2bcf_indel.c config.h $(bam2bcf_h)
+bam2depth.o: bam2depth.c config.h samtools.h $(sam_opts_h)
+bam_addrprg.o: bam_addrprg.c config.h samtools.h $(sam_opts_h)
 bam_aux.o: bam_aux.c config.h $(bam_h)
-bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h
+bam_cat.o: bam_cat.c config.h samtools.h
 bam_color.o: bam_color.c config.h $(bam_h)
-bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h)
-bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h
-bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h)
-bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h
-bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h
-bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
-bam_plcmd.o: bam_plcmd.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
-bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h)
-bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h
-bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h)
-bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h
-bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h
-bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(sam_opts_h) samtools.h
-bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h
-bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h)
+bam_import.o: bam_import.c config.h $(bam_h)
+bam_index.o: bam_index.c config.h samtools.h
+bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h)
+bam_mate.o: bam_mate.c config.h $(sam_opts_h) samtools.h
+bam_md.o: bam_md.c config.h $(sam_opts_h) samtools.h
+bam_plbuf.o: bam_plbuf.c config.h $(bam_plbuf_h)
+bam_plcmd.o: bam_plcmd.c config.h sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
+bam_quickcheck.o: bam_quickcheck.c config.h
+bam_reheader.o: bam_reheader.c config.h samtools.h
+bam_rmdup.o: bam_rmdup.c config.h $(sam_opts_h) samtools.h $(bam_h)
+bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) samtools.h
+bam_sort.o: bam_sort.c config.h $(sam_opts_h) samtools.h
+bam_split.o: bam_split.c config.h $(sam_opts_h) samtools.h
+bam_stat.o: bam_stat.c config.h samtools.h
+bam_tview.o: bam_tview.c config.h $(bam_tview_h) samtools.h $(sam_opts_h)
 bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h)
 bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h)
-bam_flags.o: bam_flags.c config.h $(htslib_sam_h)
-bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h)
-bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h
-bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h)
-bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h)
-cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h)
-dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h)
-faidx.o: faidx.c config.h $(htslib_faidx_h) samtools.h
-padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h
-phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)
-sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h)
-sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h)
+bam_flags.o: bam_flags.c config.h
+bamshuf.o: bamshuf.c config.h samtools.h $(sam_opts_h)
+bamtk.o: bamtk.c config.h samtools.h version.h
+bedcov.o: bedcov.c config.h $(sam_opts_h)
+bedidx.o: bedidx.c config.h
+cut_target.o: cut_target.c config.h samtools.h $(sam_opts_h)
+dict.o: dict.c config.h
+faidx.o: faidx.c config.h samtools.h
+padding.o: padding.c config.h sam_header.h $(sam_opts_h) samtools.h
+phase.o: phase.c config.h $(sam_opts_h) samtools.h
+sam.o: sam.c config.h $(sam_h)
+sam_header.o: sam_header.c config.h sam_header.h
 sam_opts.o: sam_opts.c config.h $(sam_opts_h)
 sam_utils.o: sam_utils.c config.h samtools.h
-sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h)
-sample.o: sample.c config.h $(sample_h) $(htslib_khash_h)
-stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h)
-stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h)
+sam_view.o: sam_view.c config.h samtools.h $(sam_opts_h)
+sample.o: sample.c config.h $(sample_h)
+stats_isize.o: stats_isize.c config.h stats_isize.h
+stats.o: stats.c config.h sam_header.h samtools.h stats_isize.h $(sam_opts_h)
 
 
 # test programs
@@ -224,30 +213,30 @@
 
 
 test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
 
 test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
 
 test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
 
 test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
 
 test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
 
 test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
 
 test/split/test_parse_args: test/split/test_parse_args.o test/test.o libst.a $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
 
 test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
 
-test_test_h = test/test.h $(htslib_sam_h)
+test_test_h = test/test.h
 
 test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h)
 test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o
@@ -256,34 +245,34 @@
 test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h)
 test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h)
 test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h)
-test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h)
-test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h)
+test/test.o: test/test.c config.h $(test_test_h)
+test/vcf-miniview.o: test/vcf-miniview.c config.h
 
 
 # misc programs
 
 misc/ace2sam: misc/ace2sam.o
-	$(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS)
 
 misc/maq2sam-short: misc/maq2sam-short.o
-	$(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS)
 
 misc/maq2sam-long: misc/maq2sam-long.o
-	$(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)
 
 misc/md5fa: misc/md5fa.o $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIBS) $(ALL_LIBS)
 
 misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIBS) $(ALL_LIBS)
 
 misc/wgsim: misc/wgsim.o
-	$(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS)
 
-misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h)
-misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h)
-misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h)
-misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h)
+misc/ace2sam.o: misc/ace2sam.c config.h
+misc/md5fa.o: misc/md5fa.c config.h
+misc/md5sum-lite.o: misc/md5sum-lite.c config.h
+misc/wgsim.o: misc/wgsim.c config.h
 
 misc/maq2sam-short.o: misc/maq2sam.c config.h
 	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c