X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bgzf.h;h=099ae9a6da1785ae132be55932a2e5c930ba49cc;hp=d5eeafe7e527c57823b8b68cb2c32511f1b0fadd;hb=016b50ab60e879a0b8f81cb76ce11ea360a03d4a;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/bgzf.h b/bgzf.h
index d5eeafe..099ae9a 100644
--- a/bgzf.h
+++ b/bgzf.h
@@ -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.
+*/
 
 #ifndef __BGZF_H
 #define __BGZF_H
@@ -94,7 +106,7 @@ int bgzf_write(BGZF* fp, const void* data, int length);
  * Return value is non-negative on success.
  * Returns -1 on error.
  */
-int64_t bgzf_tell(BGZF* fp);
+#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
 
 /*
  * Set the file to read from the location specified by pos, which must
@@ -113,8 +125,33 @@ int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
  */
 void bgzf_set_cache_size(BGZF *fp, int cache_size);
 
+int bgzf_check_EOF(BGZF *fp);
+int bgzf_read_block(BGZF* fp);
+int bgzf_flush(BGZF* fp);
+int bgzf_flush_try(BGZF *fp, int size);
+
 #ifdef __cplusplus
 }
 #endif
 
+static inline int bgzf_getc(BGZF *fp)
+{
+	int c;
+	if (fp->block_offset >= fp->block_length) {
+		if (bgzf_read_block(fp) != 0) return -2; /* error */
+		if (fp->block_length == 0) return -1; /* end-of-file */
+	}
+	c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
+    if (fp->block_offset == fp->block_length) {
+#ifdef _USE_KNETFILE
+        fp->block_address = knet_tell(fp->x.fpr);
+#else
+        fp->block_address = ftello(fp->file);
+#endif
+        fp->block_offset = 0;
+        fp->block_length = 0;
+    }
+	return c;
+}
+
 #endif