Provide a definition of ssize_t when compiling with MSVC

Define `ssize_t` within the public headers that use it, enabling them
to be compiled with MSVC, which does not provide this type definition
in its <sys/types.h> or any other headers.

Having `ssize_t` as a macro may confuse other headers, so be sure to do
this only after all other #includes and to undefine it again at the end
of each header. User code or other libraries may also have workarounds
for this issue, so checking its not already #defined and removing our
`ssize_t` macro afterwards also avoids conflicting with other workarounds.

Under MSVC, including <stdint.h>/<string.h>/etc also causes <vcruntime.h>
to be included, which defines `size_t` and `intptr_t` as unsigned/signed
versions of the same type. So we define `ssize_t` as that, if it is not
already defined (by some other workaround) and if `_INTPTR_T_DEFINED` has
indeed been defined by <vcruntime.h> (to avoid confusing error messages).

Also define it (permanently) in <htslib/hts_os.h>, unless suppressed
by defining `HTS_NO_SSIZE_T` before including the header.

htslib/bgzf.h

@@ -35,6 +35,13 @@
 
 #include "hts_defs.h"
 
+// Ensure ssize_t exists within this header. All #includes must precede this,
+// and ssize_t must be undefined again at the end of this header.
+#if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined ssize_t
+#define HTSLIB_SSIZE_T
+#define ssize_t intptr_t
+#endif
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -450,4 +457,9 @@ typedef struct BGZF BGZF;
 }
 #endif
 
+#ifdef HTSLIB_SSIZE_T
+#undef HTSLIB_SSIZE_T
+#undef ssize_t
+#endif
+
 #endif

htslib/hfile.h

@@ -32,6 +32,13 @@ DEALINGS IN THE SOFTWARE.  */
 
 #include "hts_defs.h"
 
+// Ensure ssize_t exists within this header. All #includes must precede this,
+// and ssize_t must be undefined again at the end of this header.
+#if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined ssize_t
+#define HTSLIB_SSIZE_T
+#define ssize_t intptr_t
+#endif
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -368,4 +375,9 @@ int hfile_has_plugin(const char *name);
 }
 #endif
 
+#ifdef HTSLIB_SSIZE_T
+#undef HTSLIB_SSIZE_T
+#undef ssize_t
+#endif
+
 #endif

htslib/hts_os.h

@@ -77,4 +77,10 @@ extern int is_cygpty(int fd);
 #define random rand
 #endif
 
+/* MSVC does not provide ssize_t in its <sys/types.h>. This ensures the type
+   is available (unless suppressed by defining HTS_NO_SSIZE_T first). */
+#if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined HTS_NO_SSIZE_T && !defined ssize_t
+#define ssize_t intptr_t
+#endif
+
 #endif // HTSLIB_HTS_OS_H

htslib/knetfile.h

@@ -44,6 +44,13 @@
 #define netclose(fd) closesocket(fd)
 #endif
 
+// Ensure ssize_t exists within this header. All #includes must precede this,
+// and ssize_t must be undefined again at the end of this header.
+#if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined ssize_t
+#define HTSLIB_SSIZE_T
+#define ssize_t intptr_t
+#endif
+
 // FIXME: currently I/O is unbuffered
 
 #define KNF_TYPE_LOCAL 1
@@ -102,4 +109,9 @@ extern "C" {
 }
 #endif
 
+#ifdef HTSLIB_SSIZE_T
+#undef HTSLIB_SSIZE_T
+#undef ssize_t
+#endif
+
 #endif

htslib/kstring.h

@@ -55,6 +55,13 @@
 #endif
 #endif
 
+// Ensure ssize_t exists within this header. All #includes must precede this,
+// and ssize_t must be undefined again at the end of this header.
+#if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined ssize_t
+#define HTSLIB_SSIZE_T
+#define ssize_t intptr_t
+#endif
+
 /* kstring_t is a simple non-opaque type whose fields are likely to be
  * used directly by user code (but see also ks_str() and ks_len() below).
  * A kstring_t object is initialised by either of
@@ -396,4 +403,9 @@ static inline int *ksplit(kstring_t *s, int delimiter, int *n)
 	return offsets;
 }
 
+#ifdef HTSLIB_SSIZE_T
+#undef HTSLIB_SSIZE_T
+#undef ssize_t
+#endif
+
 #endif

htslib/sam.h

@@ -33,6 +33,13 @@ DEALINGS IN THE SOFTWARE.  */
 #include "hts.h"
 #include "hts_endian.h"
 
+// Ensure ssize_t exists within this header. All #includes must precede this,
+// and ssize_t must be undefined again at the end of this header.
+#if defined _MSC_VER && defined _INTPTR_T_DEFINED && !defined ssize_t
+#define HTSLIB_SSIZE_T
+#define ssize_t intptr_t
+#endif
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -2266,4 +2273,9 @@ int bam_mods_at_qpos(const bam1_t *b, int qpos, hts_base_mod_state *state,
 }
 #endif
 
+#ifdef HTSLIB_SSIZE_T
+#undef HTSLIB_SSIZE_T
+#undef ssize_t
+#endif
+
 #endif