11e45667d4e291b3038ccda729a1cdf5bcaf004a braney Mon Jul 11 15:46:54 2016 -0700 incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX defines, modify a bunch of makefiles to include kentSrc variable pointing to top of the tree. diff --git src/htslib/hfile_internal.h src/htslib/hfile_internal.h new file mode 100644 index 0000000..47b340a --- /dev/null +++ src/htslib/hfile_internal.h @@ -0,0 +1,139 @@ +/* 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