7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/hfile_internal.h src/htslib/hfile_internal.h deleted file mode 100644 index 47b340a0678..00000000000 --- src/htslib/hfile_internal.h +++ /dev/null @@ -1,139 +0,0 @@ -/* hfile_internal.h -- internal parts of low-level input/output streams. - - Copyright (C) 2013-2015 Genome Research Ltd. - - Author: John Marshall <jm18@sanger.ac.uk> - -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" - -#ifdef __cplusplus -extern "C" { -#endif - -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; -}; - -/* 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); - - -struct hFILE_scheme_handler { - /* Opens a stream when dispatched by hopen(); should call hfile_init() - to malloc a struct "derived" from hFILE and initialise it appropriately, - including setting base.backend to its own backend vector. */ - hFILE *(*open)(const char *filename, const char *mode) HTS_RESULT_USED; - - /* Returns whether the URL denotes remote storage when dispatched by - hisremote(). For simple cases, use one of hfile_always_*() below. */ - int (*isremote)(const char *filename) HTS_RESULT_USED; - - /* The name of the plugin or other code providing this handler. */ - const char *provider; - - /* If multiple handlers are registered for the same scheme, the one with - the highest priority is used; range is 0 (lowest) to 100 (highest). */ - int priority; -}; - -/* May be used as an isremote() function in simple cases. */ -extern int hfile_always_local (const char *fname); -extern int hfile_always_remote(const char *fname); - -/* Should be called by plugins for each URL scheme they wish to handle. */ -void hfile_add_scheme_handler(const char *scheme, - const struct hFILE_scheme_handler *handler); - -struct hFILE_plugin { - /* On entry, HTSlib's plugin API version (currently 1). */ - int api_version; - - /* On entry, the plugin's handle as returned by dlopen() etc. */ - void *obj; - - /* The plugin should fill this in with its (human-readable) name. */ - const char *name; - - /* The plugin may wish to fill in a function to be called on closing. */ - void (*destroy)(void); -}; - -#ifdef ENABLE_PLUGINS -#define PLUGIN_GLOBAL(identifier,suffix) identifier - -/* Plugins must define an entry point with this signature. */ -extern int hfile_plugin_init(struct hFILE_plugin *self); - -#else -#define PLUGIN_GLOBAL(identifier,suffix) identifier##suffix - -/* Only plugins distributed within the HTSlib source that might be built - even with --disable-plugins need to use PLUGIN_GLOBAL and be listed here; - others can simply define hfile_plugin_init(). */ - -extern int hfile_plugin_init_irods(struct hFILE_plugin *self); -extern int hfile_plugin_init_libcurl(struct hFILE_plugin *self); -#endif - -/* This one is never built as a separate plugin. */ -extern int hfile_plugin_init_net(struct hFILE_plugin *self); - -#ifdef __cplusplus -} -#endif - -#endif