vcpkg/ports/htslib/0002-pthread-flag.patch

diff --git a/Makefile b/Makefile
index f6e154f..fb4f527 100644
--- a/Makefile
+++ b/Makefile
@@ -137,6 +137,8 @@ HTS_BUILD_AVX2 =
 HTS_BUILD_AVX512 =
 HTS_BUILD_SSE4 =
 
+PTHREAD = -pthread
+
 include htslib_vars.mk
 include htscodecs.mk
 
@@ -183,10 +185,10 @@ config_vars.h:
 .SUFFIXES: .bundle .c .cygdll .dll .o .pico .so
 
 .c.o:
-	$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
+	$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(PTHREAD) -c -o $@ $<
 
 .c.pico:
-	$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
+	$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(PTHREAD) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
 
 
 LIBHTS_OBJS = \
@@ -358,7 +360,7 @@ print-config:
 # file used at runtime (when $LD_LIBRARY_PATH includes the build directory).
 
 libhts.so: $(LIBHTS_OBJS:.o=.pico)
-	$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(VERSION_SCRIPT_LDFLAGS) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) -lpthread
+	$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(VERSION_SCRIPT_LDFLAGS) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) $(PTHREAD)
 	ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
 
 # Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
@@ -370,10 +372,10 @@ libhts.dylib: $(LIBHTS_OBJS)
 	ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
 
 cyghts-$(LIBHTS_SOVERSION).dll libhts.dll.a: $(LIBHTS_OBJS)
-	$(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
+	$(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) $(PTHREAD)
 
 hts-$(LIBHTS_SOVERSION).dll hts.dll.a: $(LIBHTS_OBJS)
-	$(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
+	$(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) $(PTHREAD)
 
 hts-$(LIBHTS_SOVERSION).def: hts-$(LIBHTS_SOVERSION).dll
 	gendef hts-$(LIBHTS_SOVERSION).dll
@@ -420,7 +422,7 @@ hts-object-files: $(LIBHTS_OBJS)
 # may not be able to access libhts symbols via the main program's libhts
 # if that was dynamically loaded without an explicit RTLD_GLOBAL.
 %.so: %.pico libhts.so
-	$(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< libhts.so $(LIBS) -lpthread
+	$(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< libhts.so $(LIBS) $(PTHREAD)
 
 # For programs *statically* linked to libhts.a, on macOS loading a plugin
 # linked to a shared libhts.NN.dylib would lead to conflicting duplicate
@@ -501,16 +503,16 @@ htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static3
 htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico: TARGET_CFLAGS = $(HTS_CFLAGS_SSE4)
 
 annot-tsv: annot-tsv.o libhts.a
-	$(CC) $(LDFLAGS) -o $@ annot-tsv.o libhts.a $(LIBS) -lpthread
+	$(CC) $(LDFLAGS) -o $@ annot-tsv.o libhts.a $(LIBS) $(PTHREAD)
 
 bgzip: bgzip.o libhts.a
-	$(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) -lpthread
+	$(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) $(PTHREAD)
 
 htsfile: htsfile.o libhts.a
-	$(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) -lpthread
+	$(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) $(PTHREAD)
 
 tabix: tabix.o libhts.a
-	$(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread
+	$(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) $(PTHREAD)
 
 annot-tsv.o: annot-tsv.c config.h $(htslib_hts_h) $(htslib_hts_defs_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_regidx_h)
 bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_hfile_h)