Build DLL and plugins on Cygwin

The Cygwin convention seems to be to just create cyghts-SOVER.dll
without additional symlinks, so we do that.  Linking also creates
an import library, libhts.dll.a, which plays a similar development
role to plain libhts.so; we could make this the true target of the
link rule (cf libhts.so), but currently its name will collide with
the same name used for a plain Windows import library.

NOTE: To use the plugins successfully, there must be only one copy
of libhts.a/cyghts*.dll in the complete executable.  To ensure this,
either make executables use the DLL too (so for htsfile/tabix/etc,
apply s/libhts.a/-L. -lhts/ to the recipe; FIXME) or perhaps we can
link the plugins themselves with some --allow-undefined option rather
than with the import library, as we do on other platforms.

Also ignore plain Windows *.dll for good measure.

Author: jmarshall

.gitignore

@@ -14,9 +14,13 @@ config.status
 configure
 
 hfile_*.bundle
+hfile_*.cygdll
+hfile_*.dll
 hfile_*.so
 
+cyg*.dll
 lib*.a
+lib*.dll
 lib*.dylib
 lib*.so
 lib*.so.*

Makefile

@@ -128,7 +128,7 @@ print-version:
 	@echo $(PACKAGE_VERSION)
 
 
-.SUFFIXES: .bundle .c .o .pico .so
+.SUFFIXES: .bundle .c .cygdll .dll .o .pico .so
 
 .c.o:
 	$(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $<
@@ -215,6 +215,9 @@ endif
 ifeq "$(PLATFORM)" "Darwin"
 SHLIB_FLAVOUR = dylib
 lib-shared: libhts.dylib
+else ifeq "$(findstring CYGWIN,$(PLATFORM))" "CYGWIN"
+SHLIB_FLAVOUR = cygdll
+lib-shared: cyghts-$(LIBHTS_SOVERSION).dll
 else
 SHLIB_FLAVOUR = so
 lib-shared: libhts.so
@@ -248,13 +251,19 @@ libhts.dylib: $(LIBHTS_OBJS)
 	$(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS)
 	ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
 
+cyghts-$(LIBHTS_SOVERSION).dll: $(LIBHTS_OBJS)
+	$(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import -pthread $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive -lz -lm $(LIBS)
+
 
 .pico.so:
 	$(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS)
 
 .o.bundle:
 	$(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS)
 
+.o.cygdll:
+	$(CC) -shared $(LDFLAGS) -o $@ $< libhts.dll.a $(LIBS)
+
 
 bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h)
 errmod.o errmod.pico: errmod.c config.h $(htslib_hts_h) $(htslib_ksort_h)
@@ -373,6 +382,10 @@ install-so: libhts.so installdirs
 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
 
+install-cygdll: cyghts-$(LIBHTS_SOVERSION).dll installdirs
+	$(INSTALL_PROGRAM) cyghts-$(LIBHTS_SOVERSION).dll $(DESTDIR)$(bindir)/cyghts-$(LIBHTS_SOVERSION).dll
+	$(INSTALL_PROGRAM) libhts.dll.a $(DESTDIR)$(libdir)/libhts.dll.a
+
 install-dylib: libhts.dylib installdirs
 	$(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib
 	ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib
@@ -406,6 +419,9 @@ distclean maintainer-clean: clean
 clean-so:
 	-rm -f libhts.so libhts.so.*
 
+clean-cygdll:
+	-rm -f cyghts-*.dll libhts.dll.a
+
 clean-dylib:
 	-rm -f libhts.dylib libhts.*.dylib
 
@@ -431,4 +447,5 @@ force:
 .PHONY: install install-pkgconfig installdirs lib-shared lib-static
 .PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean
 .PHONY: clean-so install-so
+.PHONY: clean-cygdll install-cygdll
 .PHONY: clean-dylib install-dylib

config.mk.in

@@ -105,6 +105,9 @@ PLUGIN_OBJS += $(plugin_OBJS)
 
 plugin.o plugin.pico: CPPFLAGS += -DPLUGINPATH=\"$(pluginpath)\"
 
+# Windows DLL plugins depend on the import library, built as a byproduct.
+$(plugin_OBJS:.o=.cygdll): cyghts-$(LIBHTS_SOVERSION).dll
+
 else
 
 LIBHTS_OBJS += $(plugin_OBJS)

configure.ac

@@ -85,6 +85,11 @@ AC_SUBST([pluginpath], $with_plugin_path)
 AC_MSG_CHECKING([shared library type])
 test -n "$host_alias" || host_alias=unknown-`uname -s`
 case $host_alias in
+  *-cygwin* | *-CYGWIN*)
+    host_result="Cygwin DLL"
+    PLATFORM=CYGWIN
+    PLUGIN_EXT=.cygdll
+    ;;
   *-darwin* | *-Darwin*)
     host_result="Darwin dylib"
     PLATFORM=Darwin