Makefile.am: ensuring that the BAM-related sources are only used if -…

…-enable-hts is specified to configure

Makefile.am

@@ -18,10 +18,15 @@ ACLOCAL_AMFLAGS = -I m4
 
 SUBDIRS := src/smithlab_cpp
 install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp, $(SUBDIRS))
-AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
-AM_CPPFLAGS += -Wall -Wextra -Wpedantic -Wno-unknown-attributes
+AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp
+if ENABLE_HTS
+AM_CPPFLAGS += -I $(top_srcdir)/src/bamxx
+endif
 
-CXXFLAGS = -O2 -DNDEBUG # default w/ optimization; careful for math
+AM_CPPFLAGS += -Wall -Wextra -Wpedantic -Wno-unknown-attributes
+if ENABLE_HTS
+AM_CPPFLAGS += -DHAVE_HTSLIB
+endif
 
 EXTRA_DIST = \
 	README.md \
@@ -47,9 +52,6 @@ TEST_EXTENSIONS = .test
 LDADD = src/smithlab_cpp/libsmithlab_cpp.a
 
 bin_PROGRAMS = preseq
-if ENABLE_HTS
-AM_CPPFLAGS += -DHAVE_HTSLIB
-endif
 
 preseq_SOURCES = \
         src/preseq.cpp \
@@ -63,14 +65,18 @@ preseq_SOURCES = \
         src/lc_extrap.cpp \
         src/bound_pop.hpp \
         src/bound_pop.cpp \
-        src/bamxx/bamxx.hpp \
         src/pop_size.hpp \
         src/pop_size.cpp \
         src/continued_fraction.hpp \
         src/continued_fraction.cpp \
-        src/bam_record_utils.hpp \
-        src/bam_record_utils.cpp \
         src/load_data_for_complexity.hpp \
         src/load_data_for_complexity.cpp \
         src/moment_sequence.hpp \
         src/moment_sequence.cpp
+
+if ENABLE_HTS
+preseq_SOURCES += \
+	src/bamxx/bamxx.hpp \
+	src/bam_record_utils.hpp \
+        src/bam_record_utils.cpp
+endif