Improve windows build.

Specifically we create the extra files needed for MSVC linkage, and
document the MSYS2/MINGW setup process.

Also added a win-dist target which attempts to produce a directory
structure suitable for binary distribution.  This isn't executed by
default, but is a good aide-memoire and to simplify testing
compatibility with things like MSVC.

Ideally we'd have a similar mechanism for all platforms to permit easy
creation of binary distributions (see samtools#533).

Author: jkbonfield

.appveyor.yml

@@ -27,7 +27,7 @@ install:
   - set MSYSTEM=MINGW64
   - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
   - set MINGWPREFIX=x86_64-w64-mingw32
-  - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-autotools mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl\""
+  - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-autotools mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl mingw-w64-x86_64-tools-git mingw-w64-x86_64-llvm\""
 
 build_script:
   - set HOME=.

INSTALL

@@ -269,3 +269,24 @@ OpenSUSE
 --------
 
 sudo zypper install autoconf automake make gcc perl zlib-devel libbz2-devel xz-devel libcurl-devel libopenssl-devel
+
+Windows MSYS2/MINGW64
+---------------------
+
+Follow MSYS2 installation instructions at
+https://www.msys2.org/wiki/MSYS2-installation/
+
+Then relaunch to MSYS2 shell using the "MSYS2 MinGW x64" executable.
+Once in that environment (check $MSYSTEM equals "MINGW64") install the
+compilers using pacman -S and the following package list:
+
+base-devel mingw-w64-x86_64-toolchain
+mingw-w64-x86_64-libdeflate mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2
+mingw-w64-x86_64-xz mingw-w64-x86_64-curl mingw-w64-x86_64-autotools
+mingw-w64-x86_64-tools-git mingw-w64-x86_64-llvm
+
+(Those last two install gendef and llvm-dlltool and are only needed
+for building libraries compatible with MSVC.)
+
+A working binary distribution may then be made using "./configure &&
+make win-dist".  Building without autoconf is not supported on Windows.

Makefile

@@ -282,10 +282,10 @@ SHLIB_FLAVOUR = cygdll
 lib-shared: cyghts-$(LIBHTS_SOVERSION).dll
 else ifeq "$(findstring MSYS,$(PLATFORM))" "MSYS"
 SHLIB_FLAVOUR = dll
-lib-shared: hts-$(LIBHTS_SOVERSION).dll
+lib-shared: hts-$(LIBHTS_SOVERSION).lib
 else ifeq "$(findstring MINGW,$(PLATFORM))" "MINGW"
 SHLIB_FLAVOUR = dll
-lib-shared: hts-$(LIBHTS_SOVERSION).dll
+lib-shared: hts-$(LIBHTS_SOVERSION).lib
 else
 SHLIB_FLAVOUR = so
 lib-shared: libhts.so
@@ -330,6 +330,40 @@ cyghts-$(LIBHTS_SOVERSION).dll libhts.dll.a: $(LIBHTS_OBJS)
 hts-$(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
 
+hts-$(LIBHTS_SOVERSION).def: hts-$(LIBHTS_SOVERSION).dll
+	gendef hts-$(LIBHTS_SOVERSION).dll
+
+hts-$(LIBHTS_SOVERSION).lib: hts-$(LIBHTS_SOVERSION).def
+	llvm-dlltool -m i386:x86-64 -d hts-$(LIBHTS_SOVERSION).def -l hts-$(LIBHTS_SOVERSION).lib
+
+# Bundling libraries, binaries, dll dependencies, and licenses into a
+# single directory.
+#
+# NOTE: only tested on the supported MSYS2/MINGW64 environment.
+dist-windows: DESTDIR=
+dist-windows: prefix=dist-windows
+dist-windows: install
+	cp hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib dist-windows/lib
+	cp `ldd hts-$(LIBHTS_SOVERSION).dll| awk '/mingw64/ {print $$3}'` dist-windows/bin
+	mkdir -p dist-windows/share/licenses/htslib
+	cp -r /mingw64/share/licenses/mingw-w64-libraries \
+	      /mingw64/share/licenses/brotli \
+	      /mingw64/share/licenses/bzip2 \
+	      /mingw64/share/licenses/gcc-libs \
+	      /mingw64/share/licenses/libdeflate \
+	      /mingw64/share/licenses/libpsl \
+	      /mingw64/share/licenses/libtre \
+	      /mingw64/share/licenses/libwinpthread \
+	      /mingw64/share/licenses/openssl \
+	      /mingw64/share/licenses/xz \
+	      /mingw64/share/licenses/zlib \
+	      /mingw64/share/licenses/zstd \
+	      dist-windows/share/licenses/
+	cp -r /usr/share/licenses/curl \
+	      dist-windows/share/licenses/
+	cp LICENSE dist-windows/share/licenses/htslib/
+
+
 # Target to allow htslib.mk to build all the object files before it
 # links the shared and static libraries.
 hts-object-files: $(LIBHTS_OBJS)