Allow tabs in the CO header field

[samtools.git] / bgzf.c

diff --git a/bgzf.c b/bgzf.c
index 71d8c81460044cb8b88c655d41ba918874641f61..59f902ff85501bade5a5a2f079ed9e8f7b52c38b 100644 (file)
--- a/bgzf.c
+++ b/bgzf.c
@@ -1,13 +1,25 @@
-/*
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT
- * This software and its documentation are copyright 2008 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
- * This software is supplied without any warranty or guaranteed support whatsoever.
- * Neither the Broad Institute nor MIT can be responsible for its use, misuse,
- * or functionality.
- */
+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+*/
 
 /*
   2009-06-29 by lh3: cache recent uncompressed blocks.
@@ -31,7 +43,7 @@ typedef struct {
 } cache_t;
 KHASH_MAP_INIT_INT64(cache, cache_t)
 
-#ifdef _NO_LFS
+#if defined(_WIN32) || defined(_MSC_VER)
 #define ftello(fp) ftell(fp)
 #define fseeko(fp, offset, whence) fseek(fp, offset, whence)
 #else
@@ -174,14 +186,20 @@ bgzf_open(const char* __restrict path, const char* __restrict mode)
                fp->open_mode = 'r';
                fp->x.fpr = file;
 #else
-               int oflag = O_RDONLY;
-               int fd = open(path, oflag);
+               int fd, oflag = O_RDONLY;
+#ifdef _WIN32
+               oflag |= O_BINARY;
+#endif
+               fd = open(path, oflag);
                if (fd == -1) return 0;
         fp = open_read(fd);
 #endif
     } else if (mode[0] == 'w' || mode[0] == 'W') {
-               int oflag = O_WRONLY | O_CREAT | O_TRUNC;
-               int fd = open(path, oflag, 0644);
+               int fd, oflag = O_WRONLY | O_CREAT | O_TRUNC;
+#ifdef _WIN32
+               oflag |= O_BINARY;
+#endif
+               fd = open(path, oflag, 0666);
                if (fd == -1) return 0;
         fp = open_write(fd, strstr(mode, "u")? 1 : 0);
     }
@@ -571,6 +589,14 @@ bgzf_close(BGZF* fp)
         if (flush_block(fp) != 0) {
             return -1;
         }
+               { // add an empty block
+                       int count, block_length = deflate_block(fp, 0);
+#ifdef _USE_KNETFILE
+                       count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
+#else
+                       count = fwrite(fp->compressed_block, 1, block_length, fp->file);
+#endif
+               }
 #ifdef _USE_KNETFILE
         if (fflush(fp->x.fpw) != 0) {
 #else
@@ -610,6 +636,25 @@ void bgzf_set_cache_size(BGZF *fp, int cache_size)
        if (fp) fp->cache_size = cache_size;
 }
 
+int bgzf_check_EOF(BGZF *fp)
+{
+       static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
+       uint8_t buf[28];
+       off_t offset;
+#ifdef _USE_KNETFILE
+       offset = knet_tell(fp->x.fpr);
+       if (knet_seek(fp->x.fpr, -28, SEEK_END) != 0) return -1;
+       knet_read(fp->x.fpr, buf, 28);
+       knet_seek(fp->x.fpr, offset, SEEK_SET);
+#else
+       offset = ftello(fp->file);
+       if (fseeko(fp->file, -28, SEEK_END) != 0) return -1;
+       fread(buf, 1, 28, fp->file);
+       fseeko(fp->file, offset, SEEK_SET);
+#endif
+       return (memcmp(magic, buf, 28) == 0)? 1 : 0;
+}
+
 int64_t
 bgzf_seek(BGZF* fp, int64_t pos, int where)
 {
@@ -636,4 +681,3 @@ bgzf_seek(BGZF* fp, int64_t pos, int where)
     fp->block_offset = block_offset;
     return 0;
 }
-