Windows compilation.

.appveyor.yml

@@ -0,0 +1,43 @@
+# version format.
+# you can use {branch} name in version format too
+# version: 1.0.{build}-{branch}
+version: 'vers.{build}'
+
+# branches to build
+branches:
+    # Whitelist
+    only:
+      - develop
+
+    # Blacklist
+    except:
+      - gh-pages
+
+# Do not build on tags (GitHub and BitBucket)
+skip_tags: true
+
+# Skipping commits affecting specific files (GitHub only). More details here: /docs/appveyor-yml
+#skip_commits:
+#  files:
+#    - docs/*
+#    - '**/*.html'
+
+# We use Mingw/Msys, so use pacman for installs
+install:
+  - set HOME=.
+  - 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-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl\""
+
+build_script:
+  - set HOME=.
+  - set MSYSTEM=MINGW64
+  - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
+  - "sh -lc \"aclocal && autoheader && autoconf && ./configure && make -j2\""
+
+#build_script:
+#  - make
+
+test_script:
+  - "sh -lc \"make test\""

.gitattributes

@@ -10,3 +10,8 @@
 .git*           export-ignore
 /.travis.yml    export-ignore
 README.md       export-ignore
+
+# Remove the text attribute from reference files, so that git doesn't convert
+# line separators on Windows machines. It causes the index files to become out
+# of sync with the fasta files.
+*.fa* -text

.gitignore

@@ -1,7 +1,9 @@
 *.o
 *.pico
+*.obj
 *.dSYM
 *.exe
+*.dll
 *.pc.tmp
 *-uninstalled.pc
 /version.h

INSTALL

@@ -48,6 +48,12 @@ library is used.  Systems that do not have CChmac will get this from
 libcrypto.  libcrypto is part of OpenSSL or one of its derivatives (LibreSSL
 or BoringSSL).
 
+On Microsoft Windows we recommend use of Mingw64/Msys2.  Note that
+currently for the test harness to work you will need to override the
+test temporary directory with e.g.: make check TEST_OPTS="-t C:/msys64/tmp/_"
+Whilst the code may work on Windows with other environments, these have
+not be verified.
+
 Building Configure
 ==================
 

Makefile

@@ -148,6 +148,7 @@ LIBHTS_OBJS = \
 	hfile.o \
 	hfile_net.o \
 	hts.o \
+	hts_os.o\
 	md5.o \
 	multipart.o \
 	probaln.o \
@@ -208,6 +209,7 @@ config.h:
 	echo '/* Default config.h generated by Makefile */' > $@
 	echo '#define HAVE_LIBBZ2 1' >> $@
 	echo '#define HAVE_LIBLZMA 1' >> $@
+	echo '#define HAVE_DRAND48 1' >> $@
 
 # And similarly for htslib.pc.tmp ("pkg-config template").  No dependency
 # on htslib.pc.in listed, as if that file is newer the usual way to regenerate
@@ -235,6 +237,9 @@ lib-shared: libhts.dylib
 else ifeq "$(findstring CYGWIN,$(PLATFORM))" "CYGWIN"
 SHLIB_FLAVOUR = cygdll
 lib-shared: cyghts-$(LIBHTS_SOVERSION).dll
+else ifeq "$(findstring MSYS,$(PLATFORM))" "MSYS"
+SHLIB_FLAVOUR = dll
+lib-shared: hts-$(LIBHTS_SOVERSION).dll
 else
 SHLIB_FLAVOUR = so
 lib-shared: libhts.so
@@ -276,6 +281,9 @@ libhts.dylib: $(LIBHTS_OBJS)
 cyghts-$(LIBHTS_SOVERSION).dll: $(LIBHTS_OBJS)
 	$(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
 
+hts-$(LIBHTS_SOVERSION).dll: $(LIBHTS_OBJS)
+	$(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
+
 
 .pico.so:
 	$(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< $(LIBS) -lpthread
@@ -286,6 +294,9 @@ cyghts-$(LIBHTS_SOVERSION).dll: $(LIBHTS_OBJS)
 .o.cygdll:
 	$(CC) -shared $(LDFLAGS) -o $@ $< libhts.dll.a $(LIBS)
 
+.o.dll:
+	$(CC) -shared $(LDFLAGS) -o $@ $< hts.dll.a $(LIBS)
+
 
 bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_thread_pool_h) cram/pooled_alloc.h $(htslib_khash_h)
 errmod.o errmod.pico: errmod.c config.h $(htslib_hts_h) $(htslib_ksort_h)
@@ -348,6 +359,9 @@ tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htsl
 
 # For tests that might use it, set $REF_PATH explicitly to use only reference
 # areas within the test suite (or set it to ':' to use no reference areas).
+#
+# If using MSYS, avoid poor shell expansion via:
+#    MSYS2_ARG_CONV_EXCL="*" make check
 check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
 	test/hts_endian
 	test/fieldarith test/fieldarith.sam
@@ -356,7 +370,7 @@ check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
 	cd test/tabix && ./test-tabix.sh tabix.tst
 	REF_PATH=: test/sam test/ce.fa test/faidx.fa
 	test/test-regidx
-	cd test && REF_PATH=: ./test.pl
+	cd test && REF_PATH=: ./test.pl $${TEST_OPTS:-}
 
 test/hts_endian: test/hts_endian.o
 	$(CC) $(LDFLAGS) -o $@ test/hts_endian.o $(LIBS)
@@ -446,6 +460,10 @@ install-cygdll: cyghts-$(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-dll: hts-$(LIBHTS_SOVERSION).dll installdirs
+	$(INSTALL_PROGRAM) hts-$(LIBHTS_SOVERSION).dll $(DESTDIR)$(bindir)/hts-$(LIBHTS_SOVERSION).dll
+	$(INSTALL_PROGRAM) hts.dll.a $(DESTDIR)$(libdir)/hts.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
@@ -483,6 +501,9 @@ clean-so:
 clean-cygdll:
 	-rm -f cyghts-*.dll libhts.dll.a
 
+clean-dll:
+	-rm -f hts-*.dll hts.dll.a
+
 clean-dylib:
 	-rm -f libhts.dylib libhts.*.dylib
 
@@ -510,4 +531,5 @@ force:
 .PHONY: tags test testclean
 .PHONY: clean-so install-so
 .PHONY: clean-cygdll install-cygdll
+.PHONY: clean-dll install-dll
 .PHONY: clean-dylib install-dylib

bgzf.c

@@ -1038,6 +1038,9 @@ static int bgzf_check_EOF_common(BGZF *fp)
     off_t offset = htell(fp->fp);
     if (hseek(fp->fp, -28, SEEK_END) < 0) {
         if (errno == ESPIPE) { hclearerr(fp->fp); return 2; }
+#ifdef _WIN32
+        if (errno == EINVAL) { hclearerr(fp->fp); return 2; }
+#endif
         else return -1;
     }
     if ( hread(fp->fp, buf, 28) != 28 ) return -1;
@@ -1179,6 +1182,7 @@ static void *bgzf_mt_reader(void *vp) {
             pthread_exit(NULL);
         }
     }
+    return NULL;
 }
 
 int bgzf_thread_pool(BGZF *fp, hts_tpool *pool, int qsize) {

bgzip.c

@@ -36,6 +36,11 @@
 #include "htslib/bgzf.h"
 #include "htslib/hts.h"
 
+#ifdef _WIN32
+#  define WIN32_LEAN_AND_MEAN
+#  include <windows.h>
+#endif
+
 static const int WINDOW_SIZE = 64 * 1024;
 
 static void error(const char *format, ...)
@@ -198,6 +203,9 @@ int main(int argc, char **argv)
 
         if ( index ) bgzf_index_build_init(fp);
         buffer = malloc(WINDOW_SIZE);
+#ifdef _WIN32
+        _setmode(f_src, O_BINARY);
+#endif
         if (rebgzip){
             if ( bgzf_index_load(fp, index_fname, NULL) < 0 ) error("Could not load index: %s.gzi\n", argv[optind]);
 
@@ -319,13 +327,21 @@ int main(int argc, char **argv)
             if ( bgzf_index_load(fp, argv[optind], ".gzi") < 0 ) error("Could not load index: %s.gzi\n", argv[optind]);
             if ( bgzf_useek(fp, start, SEEK_SET) < 0 ) error("Could not seek to %d-th (uncompressd) byte\n", start);
         }
+#ifdef _WIN32
+        _setmode(f_dst, O_BINARY);
+#endif
         while (1) {
             if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);
             else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
             if (c == 0) break;
             if (c < 0) error("Could not read %d bytes: Error %d\n", (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start), fp->errcode);
             start += c;
-            if ( write(f_dst, buffer, c) != c ) error("Could not write %d bytes\n", c);
+            if ( write(f_dst, buffer, c) != c ) {
+#ifdef _WIN32
+                if (GetLastError() != ERROR_NO_DATA)
+#endif
+                error("Could not write %d bytes\n", c);
+            }
             if (end >= 0 && start >= end) break;
         }
         free(buffer);

configure.ac

@@ -112,8 +112,8 @@ AC_ARG_ENABLE([s3],
                   [support Amazon AWS S3 URLs])],
   [], [enable_s3=check])
 
-AC_MSG_CHECKING([shared library type])
 test -n "$host_alias" || host_alias=unknown-`uname -s`
+AC_MSG_CHECKING([shared library type for $host_alias])
 case $host_alias in
   *-cygwin* | *-CYGWIN*)
     host_result="Cygwin DLL"
@@ -125,6 +125,15 @@ case $host_alias in
     PLATFORM=Darwin
     PLUGIN_EXT=.bundle
     ;;
+  *-msys* | *-MSYS* | *-mingw* | *-MINGW*)
+    host_result="MSYS dll"
+    PLATFORM=MSYS
+    PLUGIN_EXT=.dll
+    # This also sets __USE_MINGW_ANSI_STDIO which in turn makes PRId64,
+    # %lld and %z printf formats work.  It also enforces the snprintf to
+    # be C99 compliant so it returns the correct values (in kstring.c).
+    CPPFLAGS="$CPPCFLAGS -D_XOPEN_SOURCE=600"
+    ;;
   *)
     host_result="plain .so"
     PLATFORM=default
@@ -136,7 +145,7 @@ AC_SUBST([PLATFORM])
 
 dnl FIXME This pulls in dozens of standard header checks
 AC_FUNC_MMAP
-AC_CHECK_FUNCS(gmtime_r)
+AC_CHECK_FUNCS([gmtime_r fsync drand48])
 
 # Darwin has a dubious fdatasync() symbol, but no declaration in <unistd.h>
 AC_CHECK_DECL([fdatasync(int)], [AC_CHECK_FUNCS(fdatasync)])
@@ -183,9 +192,11 @@ FAILED.  This error must be resolved in order to build HTSlib successfully.])
 fi
 
 dnl connect() etc. fns are in libc on linux, but libsocket on illumos/Solaris
-libsocket=unneeded
-AC_SEARCH_LIBS(connect, socket, [libsocket=needed], [])
-
+AC_SEARCH_LIBS([recv], [socket ws2_32], [
+if test "$ac_cv_search_recv" != "none required"
+then
+  static_LIBS="$static_LIBS $ac_cv_search_recv"
+fi], [AC_MSG_ERROR([unable to find the recv() function])])
 
 if test "$enable_bz2" != no; then
   bz2_devel=ok

cram/cram_encode.c

@@ -1935,7 +1935,7 @@ static int cram_add_insertion(cram_container *c, cram_slice *s, cram_record *r,
 }
 
 /*
- * Encodes auxiliary data.
+ * Encodes auxiliary data, CRAM 1.0 format.
  * Returns the read-group parsed out of the BAM aux fields on success
  *         NULL on failure or no rg present (FIXME)
  */

cram/cram_io.c

@@ -1446,7 +1446,7 @@ char *cram_block_method2str(enum cram_block_method m) {
     case RANS0:    return "RANS0";
     case RANS1:    return "RANS1";
     case GZIP_RLE: return "GZIP_RLE";
-    case ERROR:    break;
+    case BM_ERROR: break;
     }
     return "?";
 }
@@ -3663,7 +3663,11 @@ SAM_hdr *cram_read_SAM_hdr(cram_fd *fd) {
  * Out must be at least PATH_MAX bytes long.
  */
 static void full_path(char *out, char *in) {
-    if (*in == '/') {
+    size_t in_l = strlen(in);
+    if (*in == '/' ||
+	// Windows paths
+	(in_l > 3 && toupper(*in) >= 'A'  && toupper(*in) <= 'Z' &&
+	 in[1] == ':' && (in[2] == '/' || in[2] == '\\'))) {
 	strncpy(out, in, PATH_MAX);
 	out[PATH_MAX-1] = 0;
     } else {

cram/cram_structs.h

@@ -192,7 +192,7 @@ typedef struct cram_file_def {
 struct cram_slice;
 
 enum cram_block_method {
-    ERROR    = -1,
+    BM_ERROR = -1,
     RAW      = 0,
     GZIP     = 1,
     BZIP2    = 2,

cram/mFILE.h

@@ -48,6 +48,11 @@ typedef struct {
     size_t flush_pos;
 } mFILE;
 
+// Work around a clash with winuser.h
+#ifdef MF_APPEND
+#  undef MF_APPEND
+#endif
+
 #define MF_READ    1
 #define MF_WRITE   2
 #define MF_APPEND  4

cram/os.h

@@ -205,27 +205,13 @@ static inline uint16_t le_int2(uint16_t x) {
  * Microsoft Windows running MinGW
  */
 #if defined(__MINGW32__)
-/* #define mkdir(filename,mode) mkdir((filename)) */
+#include <io.h>
+#define mkdir(filename,mode) mkdir((filename))
 #define sysconf(x) 512
-#define ftruncate(fd,len) _chsize(fd,len)
+#ifndef ftruncate
+#  define ftruncate(fd,len) _chsize(fd,len)
+#endif
 #endif
-
-/* Generic WIN32 API issues */
-#ifdef _WIN32
-#  ifndef HAVE_FSEEKO
-#    if __MSVCRT_VERSION__ >= 0x800
-       /* if you have MSVCR80 installed then you can use these definitions: */
-#      define off_t __int64
-#      define fseeko _fseeki64
-#      define ftello _ftelli64
-#    else
-       /* otherwise we're stuck with 32-bit file support */
-#      define off_t long
-#      define fseeko fseek
-#      define ftello ftell
-#    endif
-#  endif /* !HAVE_FSEEKO */
-#endif /* _WIN32 */
 
 #ifdef __cplusplus
 }

errmod.c

@@ -28,6 +28,8 @@ DEALINGS IN THE SOFTWARE.  */
 #include <math.h>
 #include "htslib/hts.h"
 #include "htslib/ksort.h"
+#include "htslib/hts_os.h" // for drand48
+
 KSORT_INIT_GENERIC(uint16_t)
 
 struct errmod_t {