libdeflate

Makefile

@@ -11,13 +11,13 @@ exec_prefix = $(prefix)
 bindir ?= $(exec_prefix)/bin
 
 # Flags
-CXX=g++
-CXXFLAGS += -isystem ${EBROOTHTSLIB} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive
-LDFLAGS += -L${EBROOTHTSLIB} -L${EBROOTHTSLIB}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time 
+CXX ?= g++
+CXXFLAGS += -std=c++11 -isystem ${EBROOTHTSLIB} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive
+LDFLAGS += -L${EBROOTHTSLIB} -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
 
 # Flags for static compile
 ifeq (${STATIC}, 1)
-	LDFLAGS += -static -static-libgcc -pthread -lhts -lz -llzma -lbz2
+	LDFLAGS += -static -static-libgcc -pthread -lhts -lz -llzma -lbz2 -ldeflate
 else
 	LDFLAGS += -lhts -lz -llzma -lbz2 -Wl,-rpath,${EBROOTHTSLIB}
 endif
@@ -47,7 +47,7 @@ TARGETS = ${SUBMODULES} ${BUILT_PROGRAMS}
 all:   	$(TARGETS)
 
 .htslib: $(HTSLIBSOURCES)
-	if [ -r src/htslib/Makefile ]; then cd src/htslib && autoheader && autoconf && ./configure --disable-s3 --disable-gcs --disable-libcurl --disable-plugins && $(MAKE) && $(MAKE) lib-static && cd ../../ && touch .htslib; fi
+	if [ -r src/htslib/Makefile ]; then cd src/htslib && autoreconf -i && ./configure --disable-s3 --disable-gcs --disable-libcurl --disable-plugins && $(MAKE) && $(MAKE) lib-static && cd ../../ && touch .htslib; fi
 
 src/sansa: ${SUBMODULES} $(SOURCES)
 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)