Author: Dylan Aïssi
Description: Use shared libs for Debian packaging.
Last-Update: 2020-03-05

--- a/makefile
+++ b/makefile
@@ -3,12 +3,12 @@
 
 #HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
 HTSLIB_INC=$(HOME)/Tools/htslib-1.11
-HTSLIB_LIB=$(HOME)/Tools/htslib-1.11/libhts.a
+HTSLIB_LIB=-lhts
 
 #BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS]
 BOOST_INC=/usr/include
-BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
-BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+BOOST_LIB_IO=-lboost_iostreams
+BOOST_LIB_PO=-lboost_program_options
 
 #HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
 #HTSLIB_INC=/software/UHTS/Analysis/samtools/1.4/include
@@ -25,12 +25,11 @@
 #CXXFLAG=-O3 -march=native
 
 #Good performance and portable on most CPUs
-CXXFLAG=-O3 -mavx2 -mfma 
+#CXXFLAG=-O3 -mavx2 -mfma 
 
 #Portable version without avx2 (much slower)
-#CXXFLAG=-O3
-
-LDFLAG=-O3
+CXXFLAG=$(CPPFLAGS) $(CXXFLAGS) -O3
+LDFLAG=$(LDFLAGS) -O3
 
 
 #DYNAMIC LIBRARIES