diff ezBAMQC/src/htslib/hfile_internal.h @ 0:dfa3745e5fd8

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/hfile_internal.h	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,76 @@
+/*  hfile_internal.h -- internal parts of low-level input/output streams.
+
+    Copyright (C) 2013-2015 Genome Research Ltd.
+
+    Author: John Marshall <[e-mail]>
+
+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 HFILE_INTERNAL_H
+#define HFILE_INTERNAL_H
+
+#include "htslib/hfile.h"
+
+struct hFILE_backend {
+    /* As per read(2), returning the number of bytes read (possibly 0) or
+       negative (and setting errno) on errors.  Front-end code will call this
+       repeatedly if necessary to attempt to get the desired byte count.  */
+    ssize_t (*read)(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED;
+
+    /* As per write(2), returning the number of bytes written or negative (and
+       setting errno) on errors.  Front-end code will call this repeatedly if
+       necessary until the desired block is written or an error occurs.  */
+    ssize_t (*write)(hFILE *fp, const void *buffer, size_t nbytes)
+        HTS_RESULT_USED;
+
+    /* As per lseek(2), returning the resulting offset within the stream or
+       negative (and setting errno) on errors.  */
+    off_t (*seek)(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED;
+
+    /* Performs low-level flushing, if any, e.g., fsync(2); for writing streams
+       only.  Returns 0 for success or negative (and sets errno) on errors. */
+    int (*flush)(hFILE *fp) HTS_RESULT_USED;
+
+    /* Closes the underlying stream (for output streams, the buffer will
+       already have been flushed), returning 0 for success or negative (and
+       setting errno) on errors, as per close(2).  */
+    int (*close)(hFILE *fp) HTS_RESULT_USED;
+};
+
+/* These are called from the hopen() dispatcher, and should call hfile_init()
+   to malloc a struct "derived" from hFILE and initialise it appropriately,
+   including setting base.backend to their own backend vector.  */
+hFILE *hopen_irods(const char *filename, const char *mode);
+hFILE *hopen_net(const char *filename, const char *mode);
+
+/* May be called by hopen_*() functions to decode a fopen()-style mode into
+   open(2)-style flags.  */
+int hfile_oflags(const char *mode);
+
+/* Must be called by hopen_*() functions to allocate the hFILE struct and set
+   up its base.  Capacity is a suggested buffer size (e.g., via fstat(2))
+   or 0 for a default-sized buffer.  */
+hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity);
+
+/* May be called by hopen_*() functions to undo the effects of hfile_init()
+   in the event opening the stream subsequently fails.  (This is safe to use
+   even if fp is NULL.  This takes care to preserve errno.)  */
+void hfile_destroy(hFILE *fp);
+
+#endif