Adding the deprecated versions of htslib_wrapper code to Makefile and Makefile.am

Author: andrewdavidsmith

Makefile

@@ -20,7 +20,7 @@
 SOURCES = $(wildcard *.cpp)
 OBJECTS = $(patsubst %.cpp, %.o, $(SOURCES))
 HEADERS = $(wildcard *.hpp)
-REQUIRES_HTSLIB = htslib_wrapper.o
+REQUIRES_HTSLIB = htslib_wrapper_deprecated.o
 
 ifndef HAVE_HTSLIB
 NO_HTSLIB := $(filter-out $(REQUIRES_HTSLIB), $(OBJECTS))

Makefile.am

@@ -28,10 +28,10 @@ chromosome_utils.cpp sim_utils.cpp smithlab_os.cpp smithlab_utils.cpp	\
 zlib_wrapper.cpp dna_four_bit.cpp
 
 if ENABLE_HTS
-libsmithlab_cpp_a_SOURCES += htslib_wrapper.cpp
+libsmithlab_cpp_a_SOURCES += htslib_wrapper_deprecated.cpp
 endif
 
 include_HEADERS = GenomicRegion.hpp MappedRead.hpp OptionParser.hpp	\
 QualityScore.hpp bisulfite_utils.hpp chromosome_utils.hpp		\
 sim_utils.hpp smithlab_os.hpp smithlab_utils.hpp zlib_wrapper.hpp	\
-htslib_wrapper.hpp dna_four_bit.hpp cigar_utils.hpp
+dna_four_bit.hpp cigar_utils.hpp htslib_wrapper_deprecated.hpp