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--- Makefile.orig 2023-08-15 19:21:58 UTC
+++ Makefile
@@ -11,14 +11,19 @@ CXXFLAGSextra ?=
# user may define the compiler
CXX ?= g++
+# user may set to '' and sed "htslib/htslib/*.h" to <htslib/*.h>
+# if they don't want the bundled htslib
+HTSLIB ?= htslib
+
# pre-defined flags
-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
+LDFLAGS_shared := -pthread -lhts -lz
+LDFLAGS_static := -static -pthread -lhts -lz
LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
LDFLAGS_gdb := $(LDFLAGS_shared)
-DATE_FMT = --iso-8601=seconds
+# --iso-8601 is not portable
+DATE_FMT = -Iseconds
ifdef SOURCE_DATE_EPOCH
BUILD_DATE ?= $(shell date -u -d "@$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u "$(DATE_FMT)")
else
@@ -41,12 +46,12 @@ GIT_BRANCH_COMMIT_DIFF := -D'GIT_BRANCH_COMMIT_DIFF="$
# Defaults, can be overridden by make arguments or environment
CXXFLAGS ?= -pipe -Wall -Wextra
-CFLAGS ?= -pipe -Wall -Wextra -O3
+CFLAGS ?= -pipe -Wall -Wextra
CXXFLAGS_SIMD ?= -mavx2
# Unconditionally set essential flags and optimization options
CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF)
-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
+CXXFLAGS_main := $(CXXFLAGS_common)
CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
##########################################################################################################
@@ -114,7 +119,7 @@ clean:
.PHONY: CLEAN
CLEAN: clean
- $(MAKE) -C htslib clean
+ $(MAKE) -C $(HTSLIB) clean
.PHONY: clean_solo
@@ -131,10 +136,10 @@ ifneq ($(MAKECMDGOALS),CLEAN)
ifneq ($(MAKECMDGOALS),clean_solo)
ifneq ($(MAKECMDGOALS),STARforMac)
ifneq ($(MAKECMDGOALS),STARforMacGDB)
-Depend.list: $(SOURCES) parametersDefault.xxd htslib
+Depend.list: $(SOURCES) parametersDefault.xxd $(HTSLIB)
echo $(SOURCES)
'rm' -f ./Depend.list
- $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) -MM $^ >> Depend.list
include Depend.list
endif
endif
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