$NetBSD: patch-Makefile,v 1.2 2023/08/29 21:49:57 bacon Exp $

# Portability

--- Makefile.orig	2022-11-01 14:50:35.000000000 +0000
+++ Makefile
@@ -11,6 +11,10 @@ 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
@@ -18,7 +22,8 @@ LDFLAGS_Mac :=-pthread -lz htslib/libhts
 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 = +%Y-%m-%dT%H:%M:%S%z
 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_
 
 # 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