gentoo-overlay/sci-biology/samtools/files/samtools-1.0-buildsystem.patch

 Makefile | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/Makefile b/Makefile
index ae59abf..0d2788c 100644
--- a/Makefile
+++ b/Makefile
@@ -21,11 +21,12 @@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC       = gcc
-CPPFLAGS = $(DFLAGS) $(INCLUDES)
-CFLAGS   = -g -Wall -O2
-LDFLAGS  =
-LDLIBS   =
+CC       ?= gcc
+CPPFLAGS += $(DFLAGS) $(INCLUDES)
+CFLAGS   ?= -g -Wall -O2
+LDFLAGS  +=
+LDLIBS   +=
+BAMLIB   ?= libbam.a
 DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
 LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
             sam_header.o bam_plbuf.o
@@ -42,6 +43,7 @@ LIBCURSES=  -lcurses # -lXCurses
 prefix      = /usr/local
 exec_prefix = $(prefix)
 bindir      = $(exec_prefix)/bin
+bindir      = $(exec_prefix)/lib
 mandir      = $(prefix)/share/man
 man1dir     = $(mandir)/man1
 
@@ -115,14 +117,22 @@ version.h:
 .c.o:
 	$(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
 
+$(LOBJS):
+	$(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
 
-lib:libbam.a
+
+lib:libbam.a libbam.so.1.0
 
 libbam.a:$(LOBJS)
 	$(AR) -csru $@ $(LOBJS)
 
-samtools: $(AOBJS) libbam.a $(HTSLIB)
-	$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
+libbam.so.1.0:$(LOBJS)
+	$(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
+	ln -sf $@ libbam.so.0
+	ln -sf $@ libbam.so
+
+samtools: $(AOBJS) $(HTSLIB) lib
+	$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
 
 bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
 bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h