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commit da5c0c7b9aa1710b70ceb2a1097101d1df1c115a Author: James Bonfield <[email protected]> Date: Tue Jul 4 13:54:58 2017 +0100 Fixes #531 from PR suggestions. - Fixed POSIX vs XOPEN macro mistake. - Sort order of Makefile. - Clearer logic of C:/path handling. - Removed fseeko from configure script and source ifdefs. NOT fixed in this update: - Removal of cram/os.h (to do later on and merge into hts_os.h). - Bgzip binary vs non-binary modes. We need clearer understanding on this, and command line extensions if we wish to support both. - fdatasync reimplementation for systems that don't have it. --- Makefile | 2 +- configure.ac | 2 +- cram/os.h | 17 ----------------- hfile.c | 9 +++++---- 4 files changed, 7 insertions(+), 23 deletions(-) diff --git a/Makefile b/Makefile index da08cbf..6379d58 100644 --- a/Makefile +++ b/Makefile @@ -138,7 +138,6 @@ print-version: LIBHTS_OBJS = \ - hts_os.o\ kfunc.o \ knetfile.o \ kstring.o \ @@ -149,6 +148,7 @@ LIBHTS_OBJS = \ hfile.o \ hfile_net.o \ hts.o \ + hts_os.o\ md5.o \ multipart.o \ probaln.o \ diff --git a/configure.ac b/configure.ac index 5cfffaa..ebedeef 100644 --- a/configure.ac +++ b/configure.ac @@ -133,7 +133,7 @@ case $host_alias in # This also sets __USE_MINGW_ANSI_STDIO which in turn makes PRId64, # %lld and %z printf formats work. It also enforces the snprintf to # be C99 compliant so it returns the correct values (in kstring.c). - CPPFLAGS="$CPPCFLAGS -D_POSIX_C_SOURCE=600" + CPPFLAGS="$CPPCFLAGS -D_XOPEN_SOURCE=600" ;; *) host_result="plain .so" diff --git a/cram/os.h b/cram/os.h index ad3d441..ba0a207 100644 --- a/cram/os.h +++ b/cram/os.h @@ -213,23 +213,6 @@ static inline uint16_t le_int2(uint16_t x) { #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 } #endif diff --git a/hfile.c b/hfile.c index ce0899e..b0c5eba 100644 --- a/hfile.c +++ b/hfile.c @@ -629,13 +629,14 @@ hFILE *hdopen(int fd, const char *mode) static hFILE *hopen_fd_fileuri(const char *url, const char *mode) { if (strncmp(url, "file://localhost/", 17) == 0) url += 16; -#ifdef _WIN32 - else if (strncmp(url, "file:///", 8) == 0) url += 8; -#else else if (strncmp(url, "file:///", 8) == 0) url += 7; -#endif else { errno = EPROTONOSUPPORT; return NULL; } +#ifdef _WIN32 + // For cases like C:/foo + if (url[0] == '/' && url[2] == ':' && url[3] == '/') url++; +#endif + return hopen_fd(url, mode); } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htslib.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
