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authorDaniel Baumann <daniel.baumann@progress-linux.org>2024-05-30 02:50:01 +0000
committerDaniel Baumann <daniel.baumann@progress-linux.org>2024-05-30 02:50:01 +0000
commit91275eb478ceb58083426099b6da3f4c7e189f19 (patch)
tree260f7d2fa77408b38c5cea96b320b9b0b6713ff2 /debian/vendor-h2o/deps/klib
parentMerging upstream version 1.9.4. (diff)
downloaddnsdist-91275eb478ceb58083426099b6da3f4c7e189f19.tar.xz
dnsdist-91275eb478ceb58083426099b6da3f4c7e189f19.zip
Merging debian version 1.9.4-1.
Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>
Diffstat (limited to '')
-rw-r--r--debian/vendor-h2o/deps/klib/README.md237
-rw-r--r--debian/vendor-h2o/deps/klib/bgzf.c555
-rw-r--r--debian/vendor-h2o/deps/klib/bgzf.h196
-rw-r--r--debian/vendor-h2o/deps/klib/kbit.h30
-rw-r--r--debian/vendor-h2o/deps/klib/kbtree.h384
-rw-r--r--debian/vendor-h2o/deps/klib/kgraph.h79
-rw-r--r--debian/vendor-h2o/deps/klib/khash.h619
-rw-r--r--debian/vendor-h2o/deps/klib/khmm.c423
-rw-r--r--debian/vendor-h2o/deps/klib/khmm.h107
-rw-r--r--debian/vendor-h2o/deps/klib/klist.h121
-rw-r--r--debian/vendor-h2o/deps/klib/kmath.c456
-rw-r--r--debian/vendor-h2o/deps/klib/kmath.h53
-rw-r--r--debian/vendor-h2o/deps/klib/knetfile.c628
-rw-r--r--debian/vendor-h2o/deps/klib/knetfile.h75
-rw-r--r--debian/vendor-h2o/deps/klib/knhx.c166
-rw-r--r--debian/vendor-h2o/deps/klib/knhx.h35
-rw-r--r--debian/vendor-h2o/deps/klib/kopen.c343
-rw-r--r--debian/vendor-h2o/deps/klib/ksa.c242
-rw-r--r--debian/vendor-h2o/deps/klib/kseq.h235
-rw-r--r--debian/vendor-h2o/deps/klib/kson.c253
-rw-r--r--debian/vendor-h2o/deps/klib/kson.h64
-rw-r--r--debian/vendor-h2o/deps/klib/ksort.h298
-rw-r--r--debian/vendor-h2o/deps/klib/kstring.c229
-rw-r--r--debian/vendor-h2o/deps/klib/kstring.h259
-rw-r--r--debian/vendor-h2o/deps/klib/ksw.c633
-rw-r--r--debian/vendor-h2o/deps/klib/ksw.h72
-rw-r--r--debian/vendor-h2o/deps/klib/kthread.c143
-rw-r--r--debian/vendor-h2o/deps/klib/kurl.c583
-rw-r--r--debian/vendor-h2o/deps/klib/kurl.h57
-rw-r--r--debian/vendor-h2o/deps/klib/kvec.h90
-rw-r--r--debian/vendor-h2o/deps/klib/lua/bio.lua149
-rw-r--r--debian/vendor-h2o/deps/klib/lua/klib.lua677
-rw-r--r--debian/vendor-h2o/deps/klib/test/Makefile60
-rw-r--r--debian/vendor-h2o/deps/klib/test/kbit_test.c137
-rw-r--r--debian/vendor-h2o/deps/klib/test/kbtree_test.c94
-rw-r--r--debian/vendor-h2o/deps/klib/test/kgraph_test.c26
-rw-r--r--debian/vendor-h2o/deps/klib/test/khash_keith.c95
-rw-r--r--debian/vendor-h2o/deps/klib/test/khash_keith2.c67
-rw-r--r--debian/vendor-h2o/deps/klib/test/khash_test.c141
-rw-r--r--debian/vendor-h2o/deps/klib/test/klist_test.c19
-rw-r--r--debian/vendor-h2o/deps/klib/test/kmin_test.c48
-rw-r--r--debian/vendor-h2o/deps/klib/test/kseq_bench.c69
-rw-r--r--debian/vendor-h2o/deps/klib/test/kseq_bench2.c43
-rw-r--r--debian/vendor-h2o/deps/klib/test/kseq_test.c27
-rw-r--r--debian/vendor-h2o/deps/klib/test/kseq_test.dat12
-rw-r--r--debian/vendor-h2o/deps/klib/test/ksort_test.c104
-rw-r--r--debian/vendor-h2o/deps/klib/test/ksort_test.cc997
-rw-r--r--debian/vendor-h2o/deps/klib/test/kstring_bench.c51
-rw-r--r--debian/vendor-h2o/deps/klib/test/kstring_bench2.c131
-rw-r--r--debian/vendor-h2o/deps/klib/test/kstring_test.c76
-rw-r--r--debian/vendor-h2o/deps/klib/test/kthread_test.c69
-rw-r--r--debian/vendor-h2o/deps/klib/test/kvec_test.cc69
52 files changed, 0 insertions, 10826 deletions
diff --git a/debian/vendor-h2o/deps/klib/README.md b/debian/vendor-h2o/deps/klib/README.md
deleted file mode 100644
index ddd74f4..0000000
--- a/debian/vendor-h2o/deps/klib/README.md
+++ /dev/null
@@ -1,237 +0,0 @@
-#Klib: a Generic Library in C
-
-##<a name="overview"></a>Overview
-
-Klib is a standalone and lightweight C library distributed under [MIT/X11
-license][1]. Most components are independent of external libraries, except the
-standard C library, and independent of each other. To use a component of this
-library, you only need to copy a couple of files to your source code tree
-without worrying about library dependencies.
-
-Klib strives for efficiency and a small memory footprint. Some components, such
-as khash.h, kbtree.h, ksort.h and kvec.h, are among the most efficient
-implementations of similar algorithms or data structures in all programming
-languages, in terms of both speed and memory use.
-
-A new documentation is available [here](http://attractivechaos.github.io/klib/)
-which includes most information in this README file.
-
-####Common components
-
-* [khash.h][khash]: generic hash table based on [double hashing][2].
-* [kbtree.h][kbtree]: generic search tree based on [B-tree][3].
-* [ksort.h][ksort]: generic sort, including [introsort][4], [merge sort][5], [heap sort][6], [comb sort][7], [Knuth shuffle][8] and the [k-small][9] algorithm.
-* [kseq.h][kseq]: generic stream buffer and a [FASTA][10]/[FASTQ][11] format parser.
-* kvec.h: generic dynamic array.
-* klist.h: generic single-linked list and [memory pool][12].
-* kstring.{h,c}: basic string library.
-* kmath.{h,c}: numerical routines including [MT19937-64][13] [pseudorandom generator][14], basic [nonlinear programming][15] and a few special math functions.
-
-####Components for more specific use cases
-
-* ksa.c: constructing [suffix arrays][16] for strings with multiple sentinels, based on a revised [SAIS algorithm][17].
-* knetfile.{h,c}: random access to remote files on HTTP or FTP.
-* kopen.c: smart stream opening.
-* khmm.{h,c}: basic [HMM][18] library.
-* ksw.(h,c}: Striped [Smith-Waterman algorithm][19].
-* knhx.{h,c}: [Newick tree format][20] parser.
-
-
-##<a name="methodology"></a>Methodology
-
-For the implementation of generic [containers][21], klib extensively uses C
-macros. To use these data structures, we usually need to instantiate methods by
-expanding a long macro. This makes the source code look unusual or even ugly
-and adds difficulty to debugging. Unfortunately, for efficient generic
-programming in C that lacks [template][22], using macros is the only
-solution. Only with macros, we can write a generic container which, once
-instantiated, compete with a type-specific container in efficiency. Some
-generic libraries in C, such as [Glib][23], use the `void*` type to implement
-containers. These implementations are usually slower and use more memory than
-klib (see [this benchmark][31]).
-
-To effectively use klib, it is important to understand how it achieves generic
-programming. We will use the hash table library as an example:
-
- #include "khash.h"
- KHASH_MAP_INIT_INT(m32, char) // instantiate structs and methods
- int main() {
- int ret, is_missing;
- khint_t k;
- khash_t(m32) *h = kh_init(m32); // allocate a hash table
- k = kh_put(m32, h, 5, &ret); // insert a key to the hash table
- if (!ret) kh_del(m32, h, k);
- kh_value(h, k) = 10; // set the value
- k = kh_get(m32, h, 10); // query the hash table
- is_missing = (k == kh_end(h)); // test if the key is present
- k = kh_get(m32, h, 5);
- kh_del(m32, h, k); // remove a key-value pair
- for (k = kh_begin(h); k != kh_end(h); ++k) // traverse
- if (kh_exist(h, k)) // test if a bucket contains data
- kh_value(h, k) = 1;
- kh_destroy(m32, h); // deallocate the hash table
- return 0;
- }
-
-In this example, the second line instantiates a hash table with `unsigned` as
-the key type and `char` as the value type. `m32` names such a type of hash table.
-All types and functions associated with this name are macros, which will be
-explained later. Macro `kh_init()` initiates a hash table and `kh_destroy()`
-frees it. `kh_put()` inserts a key and returns the iterator (or the position)
-in the hash table. `kh_get()` and `kh_del()` get a key and delete an element,
-respectively. Macro `kh_exist()` tests if an iterator (or a position) is filled
-with data.
-
-An immediate question is this piece of code does not look like a valid C
-program (e.g. lacking semicolon, assignment to an _apparent_ function call and
-_apparent_ undefined `m32` 'variable'). To understand why the code is correct,
-let's go a bit further into the source code of `khash.h`, whose skeleton looks
-like:
-
- #define KHASH_INIT(name, SCOPE, key_t, val_t, is_map, _hashf, _hasheq) \
- typedef struct { \
- int n_buckets, size, n_occupied, upper_bound; \
- unsigned *flags; \
- key_t *keys; \
- val_t *vals; \
- } kh_##name##_t; \
- SCOPE inline kh_##name##_t *init_##name() { \
- return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t)); \
- } \
- SCOPE inline int get_##name(kh_##name##_t *h, key_t k) \
- ... \
- SCOPE inline void destroy_##name(kh_##name##_t *h) { \
- if (h) { \
- free(h->keys); free(h->flags); free(h->vals); free(h); \
- } \
- }
-
- #define _int_hf(key) (unsigned)(key)
- #define _int_heq(a, b) (a == b)
- #define khash_t(name) kh_##name##_t
- #define kh_value(h, k) ((h)->vals[k])
- #define kh_begin(h, k) 0
- #define kh_end(h) ((h)->n_buckets)
- #define kh_init(name) init_##name()
- #define kh_get(name, h, k) get_##name(h, k)
- #define kh_destroy(name, h) destroy_##name(h)
- ...
- #define KHASH_MAP_INIT_INT(name, val_t) \
- KHASH_INIT(name, static, unsigned, val_t, is_map, _int_hf, _int_heq)
-
-`KHASH_INIT()` is a huge macro defining all the structs and methods. When this
-macro is called, all the code inside it will be inserted by the [C
-preprocess][37] to the place where it is called. If the macro is called
-multiple times, multiple copies of the code will be inserted. To avoid naming
-conflict of hash tables with different key-value types, the library uses [token
-concatenation][36], which is a preprocessor feature whereby we can substitute
-part of a symbol based on the parameter of the macro. In the end, the C
-preprocessor will generate the following code and feed it to the compiler
-(macro `kh_exist(h,k)` is a little complex and not expanded for simplicity):
-
- typedef struct {
- int n_buckets, size, n_occupied, upper_bound;
- unsigned *flags;
- unsigned *keys;
- char *vals;
- } kh_m32_t;
- static inline kh_m32_t *init_m32() {
- return (kh_m32_t*)calloc(1, sizeof(kh_m32_t));
- }
- static inline int get_m32(kh_m32_t *h, unsigned k)
- ...
- static inline void destroy_m32(kh_m32_t *h) {
- if (h) {
- free(h->keys); free(h->flags); free(h->vals); free(h);
- }
- }
-
- int main() {
- int ret, is_missing;
- khint_t k;
- kh_m32_t *h = init_m32();
- k = put_m32(h, 5, &ret);
- if (!ret) del_m32(h, k);
- h->vals[k] = 10;
- k = get_m32(h, 10);
- is_missing = (k == h->n_buckets);
- k = get_m32(h, 5);
- del_m32(h, k);
- for (k = 0; k != h->n_buckets; ++k)
- if (kh_exist(h, k)) h->vals[k] = 1;
- destroy_m32(h);
- return 0;
- }
-
-This is the C program we know.
-
-From this example, we can see that macros and the C preprocessor plays a key
-role in klib. Klib is fast partly because the compiler knows the key-value
-type at the compile time and is able to optimize the code to the same level
-as type-specific code. A generic library written with `void*` will not get such
-performance boost.
-
-Massively inserting code upon instantiation may remind us of C++'s slow
-compiling speed and huge binary size when STL/boost is in use. Klib is much
-better in this respect due to its small code size and component independency.
-Inserting several hundreds lines of code won't make compiling obviously slower.
-
-##<a name="resources"></a>Resources
-
-* Library documentation, if present, is available in the header files. Examples
-can be found in the [test/][24] directory.
-* **Obsolete** documentation of the hash table library can be found at
-[SourceForge][25]. This README is partly adapted from the old documentation.
-* [Blog post][26] describing the hash table library.
-* [Blog post][27] on why using `void*` for generic programming may be inefficient.
-* [Blog post][28] on the generic stream buffer.
-* [Blog post][29] evaluating the performance of `kvec.h`.
-* [Blog post][30] arguing B-tree may be a better data structure than a binary search tree.
-* [Blog post][31] evaluating the performance of `khash.h` and `kbtree.h` among many other implementations.
-[An older version][33] of the benchmark is also available.
-* [Blog post][34] benchmarking internal sorting algorithms and implementations.
-* [Blog post][32] on the k-small algorithm.
-* [Blog post][35] on the Hooke-Jeeve's algorithm for nonlinear programming.
-
-[1]: http://en.wikipedia.org/wiki/MIT_License
-[2]: http://en.wikipedia.org/wiki/Double_hashing
-[3]: http://en.wikipedia.org/wiki/B-tree
-[4]: http://en.wikipedia.org/wiki/Introsort
-[5]: http://en.wikipedia.org/wiki/Merge_sort
-[6]: http://en.wikipedia.org/wiki/Heapsort
-[7]: http://en.wikipedia.org/wiki/Comb_sort
-[8]: http://en.wikipedia.org/wiki/Fisher-Yates_shuffle
-[9]: http://en.wikipedia.org/wiki/Selection_algorithm
-[10]: http://en.wikipedia.org/wiki/FASTA_format
-[11]: http://en.wikipedia.org/wiki/FASTQ_format
-[12]: http://en.wikipedia.org/wiki/Memory_pool
-[13]: http://en.wikipedia.org/wiki/Mersenne_twister
-[14]: http://en.wikipedia.org/wiki/Pseudorandom_generator
-[15]: http://en.wikipedia.org/wiki/Nonlinear_programming
-[16]: http://en.wikipedia.org/wiki/Suffix_array
-[17]: https://sites.google.com/site/yuta256/sais
-[18]: http://en.wikipedia.org/wiki/Hidden_Markov_model
-[19]: http://en.wikipedia.org/wiki/Smith-Waterman_algorithm
-[20]: http://en.wikipedia.org/wiki/Newick_format
-[21]: http://en.wikipedia.org/wiki/Container_(abstract_data_type)
-[22]: http://en.wikipedia.org/wiki/Template_(C%2B%2B)
-[23]: http://en.wikipedia.org/wiki/GLib
-[24]: https://github.com/attractivechaos/klib/tree/master/test
-[25]: http://klib.sourceforge.net/
-[26]: http://attractivechaos.wordpress.com/2008/09/02/implementing-generic-hash-library-in-c/
-[27]: http://attractivechaos.wordpress.com/2008/10/02/using-void-in-generic-c-programming-may-be-inefficient/
-[28]: http://attractivechaos.wordpress.com/2008/10/11/a-generic-buffered-stream-wrapper/
-[29]: http://attractivechaos.wordpress.com/2008/09/19/c-array-vs-c-vector/
-[30]: http://attractivechaos.wordpress.com/2008/09/24/b-tree-vs-binary-search-tree/
-[31]: http://attractivechaos.wordpress.com/2008/10/07/another-look-at-my-old-benchmark/
-[32]: http://attractivechaos.wordpress.com/2008/09/13/calculating-median/
-[33]: http://attractivechaos.wordpress.com/2008/08/28/comparison-of-hash-table-libraries/
-[34]: http://attractivechaos.wordpress.com/2008/08/28/comparison-of-internal-sorting-algorithms/
-[35]: http://attractivechaos.wordpress.com/2008/08/24/derivative-free-optimization-dfo/
-[36]: http://en.wikipedia.org/wiki/C_preprocessor#Token_concatenation
-[37]: http://en.wikipedia.org/wiki/C_preprocessor
-
-[kbtree]: http://attractivechaos.github.io/klib/#KBtree%3A%20generic%20ordered%20map:%5B%5BKBtree%3A%20generic%20ordered%20map%5D%5D
-[khash]: http://attractivechaos.github.io/klib/#Khash%3A%20generic%20hash%20table:%5B%5BKhash%3A%20generic%20hash%20table%5D%5D
-[kseq]: http://attractivechaos.github.io/klib/#Kseq%3A%20stream%20buffer%20and%20FASTA%2FQ%20parser:%5B%5BKseq%3A%20stream%20buffer%20and%20FASTA%2FQ%20parser%5D%5D
-[ksort]: http://attractivechaos.github.io/klib/#Ksort%3A%20sorting%2C%20shuffling%2C%20heap%20and%20k-small:%5B%5BKsort%3A%20sorting%2C%20shuffling%2C%20heap%20and%20k-small%5D%5D
diff --git a/debian/vendor-h2o/deps/klib/bgzf.c b/debian/vendor-h2o/deps/klib/bgzf.c
deleted file mode 100644
index 9833414..0000000
--- a/debian/vendor-h2o/deps/klib/bgzf.c
+++ /dev/null
@@ -1,555 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
- 2011 Attractive Chaos <attractor@live.co.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.
-*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
-#include <assert.h>
-#include <sys/types.h>
-#include "bgzf.h"
-
-#ifdef _USE_KNETFILE
-#include "knetfile.h"
-typedef knetFile *_bgzf_file_t;
-#define _bgzf_open(fn, mode) knet_open(fn, mode)
-#define _bgzf_dopen(fp, mode) knet_dopen(fp, mode)
-#define _bgzf_close(fp) knet_close(fp)
-#define _bgzf_fileno(fp) ((fp)->fd)
-#define _bgzf_tell(fp) knet_tell(fp)
-#define _bgzf_seek(fp, offset, whence) knet_seek(fp, offset, whence)
-#define _bgzf_read(fp, buf, len) knet_read(fp, buf, len)
-#define _bgzf_write(fp, buf, len) knet_write(fp, buf, len)
-#else // ~defined(_USE_KNETFILE)
-#if defined(_WIN32) || defined(_MSC_VER)
-#define ftello(fp) ftell(fp)
-#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
-#else // ~defined(_WIN32)
-extern off_t ftello(FILE *stream);
-extern int fseeko(FILE *stream, off_t offset, int whence);
-#endif // ~defined(_WIN32)
-typedef FILE *_bgzf_file_t;
-#define _bgzf_open(fn, mode) fopen(fn, mode)
-#define _bgzf_dopen(fp, mode) fdopen(fp, mode)
-#define _bgzf_close(fp) fclose(fp)
-#define _bgzf_fileno(fp) fileno(fp)
-#define _bgzf_tell(fp) ftello(fp)
-#define _bgzf_seek(fp, offset, whence) fseeko(fp, offset, whence)
-#define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp)
-#define _bgzf_write(fp, buf, len) fwrite(buf, 1, len, fp)
-#endif // ~define(_USE_KNETFILE)
-
-#define BLOCK_HEADER_LENGTH 18
-#define BLOCK_FOOTER_LENGTH 8
-
-/* BGZF/GZIP header (speciallized from RFC 1952; little endian):
- +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
- | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN|
- +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
-*/
-static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0";
-
-#ifdef BGZF_CACHE
-typedef struct {
- int size;
- uint8_t *block;
- int64_t end_offset;
-} cache_t;
-#include "khash.h"
-KHASH_MAP_INIT_INT64(cache, cache_t)
-#endif
-
-static inline void packInt16(uint8_t *buffer, uint16_t value)
-{
- buffer[0] = value;
- buffer[1] = value >> 8;
-}
-
-static inline int unpackInt16(const uint8_t *buffer)
-{
- return buffer[0] | buffer[1] << 8;
-}
-
-static inline void packInt32(uint8_t *buffer, uint32_t value)
-{
- buffer[0] = value;
- buffer[1] = value >> 8;
- buffer[2] = value >> 16;
- buffer[3] = value >> 24;
-}
-
-static BGZF *bgzf_read_init()
-{
- BGZF *fp;
- fp = calloc(1, sizeof(BGZF));
- fp->open_mode = 'r';
- fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
- fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
-#ifdef BGZF_CACHE
- fp->cache = kh_init(cache);
-#endif
- return fp;
-}
-
-static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level
-{
- BGZF *fp;
- fp = calloc(1, sizeof(BGZF));
- fp->open_mode = 'w';
- fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
- fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
- fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
- if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
- return fp;
-}
-// get the compress level from the mode string
-static int mode2level(const char *__restrict mode)
-{
- int i, compress_level = -1;
- for (i = 0; mode[i]; ++i)
- if (mode[i] >= '0' && mode[i] <= '9') break;
- if (mode[i]) compress_level = (int)mode[i] - '0';
- if (strchr(mode, 'u')) compress_level = 0;
- return compress_level;
-}
-
-BGZF *bgzf_open(const char *path, const char *mode)
-{
- BGZF *fp = 0;
- if (strchr(mode, 'r') || strchr(mode, 'R')) {
- _bgzf_file_t fpr;
- if ((fpr = _bgzf_open(path, "r")) == 0) return 0;
- fp = bgzf_read_init();
- fp->fp = fpr;
- } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
- FILE *fpw;
- if ((fpw = fopen(path, "w")) == 0) return 0;
- fp = bgzf_write_init(mode2level(mode));
- fp->fp = fpw;
- }
- return fp;
-}
-
-BGZF *bgzf_dopen(int fd, const char *mode)
-{
- BGZF *fp = 0;
- if (strchr(mode, 'r') || strchr(mode, 'R')) {
- _bgzf_file_t fpr;
- if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0;
- fp = bgzf_read_init();
- fp->fp = fpr;
- } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
- FILE *fpw;
- if ((fpw = fdopen(fd, "w")) == 0) return 0;
- fp = bgzf_write_init(mode2level(mode));
- fp->fp = fpw;
- }
- return fp;
-}
-
-// Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length.
-static int deflate_block(BGZF *fp, int block_length)
-{
- uint8_t *buffer = fp->compressed_block;
- int buffer_size = BGZF_BLOCK_SIZE;
- int input_length = block_length;
- int compressed_length = 0;
- int remaining;
- uint32_t crc;
-
- assert(block_length <= BGZF_BLOCK_SIZE); // guaranteed by the caller
- memcpy(buffer, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block
- while (1) { // loop to retry for blocks that do not compress enough
- int status;
- z_stream zs;
- zs.zalloc = NULL;
- zs.zfree = NULL;
- zs.next_in = fp->uncompressed_block;
- zs.avail_in = input_length;
- zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
- zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
- status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY); // -15 to disable zlib header/footer
- if (status != Z_OK) {
- fp->errcode |= BGZF_ERR_ZLIB;
- return -1;
- }
- status = deflate(&zs, Z_FINISH);
- if (status != Z_STREAM_END) { // not compressed enough
- deflateEnd(&zs); // reset the stream
- if (status == Z_OK) { // reduce the size and recompress
- input_length -= 1024;
- assert(input_length > 0); // logically, this should not happen
- continue;
- }
- fp->errcode |= BGZF_ERR_ZLIB;
- return -1;
- }
- if (deflateEnd(&zs) != Z_OK) {
- fp->errcode |= BGZF_ERR_ZLIB;
- return -1;
- }
- compressed_length = zs.total_out;
- compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
- assert(compressed_length <= BGZF_BLOCK_SIZE);
- break;
- }
-
- assert(compressed_length > 0);
- packInt16((uint8_t*)&buffer[16], compressed_length - 1); // write the compressed_length; -1 to fit 2 bytes
- crc = crc32(0L, NULL, 0L);
- crc = crc32(crc, fp->uncompressed_block, input_length);
- packInt32((uint8_t*)&buffer[compressed_length-8], crc);
- packInt32((uint8_t*)&buffer[compressed_length-4], input_length);
-
- remaining = block_length - input_length;
- if (remaining > 0) {
- assert(remaining <= input_length);
- memcpy(fp->uncompressed_block, fp->uncompressed_block + input_length, remaining);
- }
- fp->block_offset = remaining;
- return compressed_length;
-}
-
-// Inflate the block in fp->compressed_block into fp->uncompressed_block
-static int inflate_block(BGZF* fp, int block_length)
-{
- z_stream zs;
- zs.zalloc = NULL;
- zs.zfree = NULL;
- zs.next_in = fp->compressed_block + 18;
- zs.avail_in = block_length - 16;
- zs.next_out = fp->uncompressed_block;
- zs.avail_out = BGZF_BLOCK_SIZE;
-
- if (inflateInit2(&zs, -15) != Z_OK) {
- fp->errcode |= BGZF_ERR_ZLIB;
- return -1;
- }
- if (inflate(&zs, Z_FINISH) != Z_STREAM_END) {
- inflateEnd(&zs);
- fp->errcode |= BGZF_ERR_ZLIB;
- return -1;
- }
- if (inflateEnd(&zs) != Z_OK) {
- fp->errcode |= BGZF_ERR_ZLIB;
- return -1;
- }
- return zs.total_out;
-}
-
-static int check_header(const uint8_t *header)
-{
- return (header[0] == 31 && header[1] == 139 && header[2] == 8 && (header[3] & 4) != 0
- && unpackInt16((uint8_t*)&header[10]) == 6
- && header[12] == 'B' && header[13] == 'C'
- && unpackInt16((uint8_t*)&header[14]) == 2);
-}
-
-#ifdef BGZF_CACHE
-static void free_cache(BGZF *fp)
-{
- khint_t k;
- khash_t(cache) *h = (khash_t(cache)*)fp->cache;
- if (fp->open_mode != 'r') return;
- for (k = kh_begin(h); k < kh_end(h); ++k)
- if (kh_exist(h, k)) free(kh_val(h, k).block);
- kh_destroy(cache, h);
-}
-
-static int load_block_from_cache(BGZF *fp, int64_t block_address)
-{
- khint_t k;
- cache_t *p;
- khash_t(cache) *h = (khash_t(cache)*)fp->cache;
- k = kh_get(cache, h, block_address);
- if (k == kh_end(h)) return 0;
- p = &kh_val(h, k);
- if (fp->block_length != 0) fp->block_offset = 0;
- fp->block_address = block_address;
- fp->block_length = p->size;
- memcpy(fp->uncompressed_block, p->block, BGZF_BLOCK_SIZE);
- _bgzf_seek((_bgzf_file_t)fp->fp, p->end_offset, SEEK_SET);
- return p->size;
-}
-
-static void cache_block(BGZF *fp, int size)
-{
- int ret;
- khint_t k;
- cache_t *p;
- khash_t(cache) *h = (khash_t(cache)*)fp->cache;
- if (BGZF_BLOCK_SIZE >= fp->cache_size) return;
- if ((kh_size(h) + 1) * BGZF_BLOCK_SIZE > fp->cache_size) {
- /* A better way would be to remove the oldest block in the
- * cache, but here we remove a random one for simplicity. This
- * should not have a big impact on performance. */
- for (k = kh_begin(h); k < kh_end(h); ++k)
- if (kh_exist(h, k)) break;
- if (k < kh_end(h)) {
- free(kh_val(h, k).block);
- kh_del(cache, h, k);
- }
- }
- k = kh_put(cache, h, fp->block_address, &ret);
- if (ret == 0) return; // if this happens, a bug!
- p = &kh_val(h, k);
- p->size = fp->block_length;
- p->end_offset = fp->block_address + size;
- p->block = malloc(BGZF_BLOCK_SIZE);
- memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_BLOCK_SIZE);
-}
-#else
-static void free_cache(BGZF *fp) {}
-static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;}
-static void cache_block(BGZF *fp, int size) {}
-#endif
-
-int bgzf_read_block(BGZF *fp)
-{
- uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block;
- int count, size = 0, block_length, remaining;
- int64_t block_address;
- block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
- if (load_block_from_cache(fp, block_address)) return 0;
- count = _bgzf_read(fp->fp, header, sizeof(header));
- if (count == 0) { // no data read
- fp->block_length = 0;
- return 0;
- }
- if (count != sizeof(header) || !check_header(header)) {
- fp->errcode |= BGZF_ERR_HEADER;
- return -1;
- }
- size = count;
- block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1"
- compressed_block = (uint8_t*)fp->compressed_block;
- memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
- remaining = block_length - BLOCK_HEADER_LENGTH;
- count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
- if (count != remaining) {
- fp->errcode |= BGZF_ERR_IO;
- return -1;
- }
- size += count;
- if ((count = inflate_block(fp, block_length)) < 0) return -1;
- if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek.
- fp->block_address = block_address;
- fp->block_length = count;
- cache_block(fp, size);
- return 0;
-}
-
-ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length)
-{
- ssize_t bytes_read = 0;
- uint8_t *output = data;
- if (length <= 0) return 0;
- assert(fp->open_mode == 'r');
- while (bytes_read < length) {
- int copy_length, available = fp->block_length - fp->block_offset;
- uint8_t *buffer;
- if (available <= 0) {
- if (bgzf_read_block(fp) != 0) return -1;
- available = fp->block_length - fp->block_offset;
- if (available <= 0) break;
- }
- copy_length = length - bytes_read < available? length - bytes_read : available;
- buffer = fp->uncompressed_block;
- memcpy(output, buffer + fp->block_offset, copy_length);
- fp->block_offset += copy_length;
- output += copy_length;
- bytes_read += copy_length;
- }
- if (fp->block_offset == fp->block_length) {
- fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
- fp->block_offset = fp->block_length = 0;
- }
- return bytes_read;
-}
-
-int bgzf_flush(BGZF *fp)
-{
- assert(fp->open_mode == 'w');
- while (fp->block_offset > 0) {
- int block_length;
- block_length = deflate_block(fp, fp->block_offset);
- if (block_length < 0) return -1;
- if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) {
- fp->errcode |= BGZF_ERR_IO; // possibly truncated file
- return -1;
- }
- fp->block_address += block_length;
- }
- return 0;
-}
-
-int bgzf_flush_try(BGZF *fp, ssize_t size)
-{
- if (fp->block_offset + size > BGZF_BLOCK_SIZE)
- return bgzf_flush(fp);
- return -1;
-}
-
-ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length)
-{
- const uint8_t *input = data;
- int block_length = BGZF_BLOCK_SIZE, bytes_written;
- assert(fp->open_mode == 'w');
- input = data;
- bytes_written = 0;
- while (bytes_written < length) {
- uint8_t* buffer = fp->uncompressed_block;
- int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written;
- memcpy(buffer + fp->block_offset, input, copy_length);
- fp->block_offset += copy_length;
- input += copy_length;
- bytes_written += copy_length;
- if (fp->block_offset == block_length && bgzf_flush(fp)) break;
- }
- return bytes_written;
-}
-
-int bgzf_close(BGZF* fp)
-{
- int ret, count, block_length;
- if (fp == 0) return -1;
- if (fp->open_mode == 'w') {
- if (bgzf_flush(fp) != 0) return -1;
- block_length = deflate_block(fp, 0); // write an empty block
- count = fwrite(fp->compressed_block, 1, block_length, fp->fp);
- if (fflush(fp->fp) != 0) {
- fp->errcode |= BGZF_ERR_IO;
- return -1;
- }
- }
- ret = fp->open_mode == 'w'? fclose(fp->fp) : _bgzf_close(fp->fp);
- if (ret != 0) return -1;
- free(fp->uncompressed_block);
- free(fp->compressed_block);
- free_cache(fp);
- free(fp);
- return 0;
-}
-
-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;
- offset = _bgzf_tell((_bgzf_file_t)fp->fp);
- if (_bgzf_seek(fp->fp, -28, SEEK_END) < 0) return 0;
- _bgzf_read(fp->fp, buf, 28);
- _bgzf_seek(fp->fp, offset, SEEK_SET);
- return (memcmp(magic, buf, 28) == 0)? 1 : 0;
-}
-
-int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
-{
- int block_offset;
- int64_t block_address;
-
- if (fp->open_mode != 'r' || where != SEEK_SET) {
- fp->errcode |= BGZF_ERR_MISUSE;
- return -1;
- }
- block_offset = pos & 0xFFFF;
- block_address = pos >> 16;
- if (_bgzf_seek(fp->fp, block_address, SEEK_SET) < 0) {
- fp->errcode |= BGZF_ERR_IO;
- return -1;
- }
- fp->block_length = 0; // indicates current block has not been loaded
- fp->block_address = block_address;
- fp->block_offset = block_offset;
- return 0;
-}
-
-int bgzf_is_bgzf(const char *fn)
-{
- uint8_t buf[16];
- int n;
- _bgzf_file_t fp;
- if ((fp = _bgzf_open(fn, "r")) == 0) return 0;
- n = _bgzf_read(fp, buf, 16);
- _bgzf_close(fp);
- if (n != 16) return 0;
- return memcmp(g_magic, buf, 16) == 0? 1 : 0;
-}
-
-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) {
- fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
- fp->block_offset = 0;
- fp->block_length = 0;
- }
- return c;
-}
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-int bgzf_getline(BGZF *fp, int delim, kstring_t *str)
-{
- int l, state = 0;
- unsigned char *buf = (unsigned char*)fp->uncompressed_block;
- str->l = 0;
- do {
- if (fp->block_offset >= fp->block_length) {
- if (bgzf_read_block(fp) != 0) { state = -2; break; }
- if (fp->block_length == 0) { state = -1; break; }
- }
- for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l);
- if (l < fp->block_length) state = 1;
- l -= fp->block_offset;
- if (str->l + l + 1 >= str->m) {
- str->m = str->l + l + 2;
- kroundup32(str->m);
- str->s = (char*)realloc(str->s, str->m);
- }
- memcpy(str->s + str->l, buf + fp->block_offset, l);
- str->l += l;
- fp->block_offset += l + 1;
- if (fp->block_offset >= fp->block_length) {
- fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
- fp->block_offset = 0;
- fp->block_length = 0;
- }
- } while (state == 0);
- if (str->l == 0 && state < 0) return state;
- str->s[str->l] = 0;
- return str->l;
-}
diff --git a/debian/vendor-h2o/deps/klib/bgzf.h b/debian/vendor-h2o/deps/klib/bgzf.h
deleted file mode 100644
index 29fe0e5..0000000
--- a/debian/vendor-h2o/deps/klib/bgzf.h
+++ /dev/null
@@ -1,196 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
- 2011 Attractive Chaos <attractor@live.co.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.
-*/
-
-/* The BGZF library was originally written by Bob Handsaker from the Broad
- * Institute. It was later improved by the SAMtools developers. */
-
-#ifndef __BGZF_H
-#define __BGZF_H
-
-#include <stdint.h>
-#include <stdio.h>
-#include <zlib.h>
-
-#define BGZF_BLOCK_SIZE 0x10000
-#define BGZF_MAX_BLOCK_SIZE 0x10000
-
-#define BGZF_ERR_ZLIB 1
-#define BGZF_ERR_HEADER 2
-#define BGZF_ERR_IO 4
-#define BGZF_ERR_MISUSE 8
-
-typedef struct {
- int open_mode:8, compress_level:8, errcode:16;
- int cache_size;
- int block_length, block_offset;
- int64_t block_address;
- void *uncompressed_block, *compressed_block;
- void *cache; // a pointer to a hash table
- void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading
-} BGZF;
-
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct __kstring_t {
- size_t l, m;
- char *s;
-} kstring_t;
-#endif
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- /******************
- * Basic routines *
- ******************/
-
- /**
- * Open an existing file descriptor for reading or writing.
- *
- * @param fd file descriptor
- * @param mode mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies
- * the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored.
- * @return BGZF file handler; 0 on error
- */
- BGZF* bgzf_dopen(int fd, const char *mode);
-
- #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility
-
- /**
- * Open the specified file for reading or writing.
- */
- BGZF* bgzf_open(const char* path, const char *mode);
-
- /**
- * Close the BGZF and free all associated resources.
- *
- * @param fp BGZF file handler
- * @return 0 on success and -1 on error
- */
- int bgzf_close(BGZF *fp);
-
- /**
- * Read up to _length_ bytes from the file storing into _data_.
- *
- * @param fp BGZF file handler
- * @param data data array to read into
- * @param length size of data to read
- * @return number of bytes actually read; 0 on end-of-file and -1 on error
- */
- ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length);
-
- /**
- * Write _length_ bytes from _data_ to the file.
- *
- * @param fp BGZF file handler
- * @param data data array to write
- * @param length size of data to write
- * @return number of bytes actually written; -1 on error
- */
- ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length);
-
- /**
- * Write the data in the buffer to the file.
- */
- int bgzf_flush(BGZF *fp);
-
- /**
- * Return a virtual file pointer to the current location in the file.
- * No interpetation of the value should be made, other than a subsequent
- * call to bgzf_seek can be used to position the file at the same point.
- * Return value is non-negative on success.
- */
- #define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
-
- /**
- * Set the file to read from the location specified by _pos_.
- *
- * @param fp BGZF file handler
- * @param pos virtual file offset returned by bgzf_tell()
- * @param whence must be SEEK_SET
- * @return 0 on success and -1 on error
- */
- int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence);
-
- /**
- * Check if the BGZF end-of-file (EOF) marker is present
- *
- * @param fp BGZF file handler opened for reading
- * @return 1 if EOF is present; 0 if not or on I/O error
- */
- int bgzf_check_EOF(BGZF *fp);
-
- /**
- * Check if a file is in the BGZF format
- *
- * @param fn file name
- * @return 1 if _fn_ is BGZF; 0 if not or on I/O error
- */
- int bgzf_is_bgzf(const char *fn);
-
- /*********************
- * Advanced routines *
- *********************/
-
- /**
- * Set the cache size. Only effective when compiled with -DBGZF_CACHE.
- *
- * @param fp BGZF file handler
- * @param size size of cache in bytes; 0 to disable caching (default)
- */
- void bgzf_set_cache_size(BGZF *fp, int size);
-
- /**
- * Flush the file if the remaining buffer size is smaller than _size_
- */
- int bgzf_flush_try(BGZF *fp, ssize_t size);
-
- /**
- * Read one byte from a BGZF file. It is faster than bgzf_read()
- * @param fp BGZF file handler
- * @return byte read; -1 on end-of-file or error
- */
- int bgzf_getc(BGZF *fp);
-
- /**
- * Read one line from a BGZF file. It is faster than bgzf_getc()
- *
- * @param fp BGZF file handler
- * @param delim delimitor
- * @param str string to write to; must be initialized
- * @return length of the string; 0 on end-of-file; negative on error
- */
- int bgzf_getline(BGZF *fp, int delim, kstring_t *str);
-
- /**
- * Read the next BGZF block.
- */
- int bgzf_read_block(BGZF *fp);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kbit.h b/debian/vendor-h2o/deps/klib/kbit.h
deleted file mode 100644
index 3793cf8..0000000
--- a/debian/vendor-h2o/deps/klib/kbit.h
+++ /dev/null
@@ -1,30 +0,0 @@
-#ifndef KBIT_H
-#define KBIT_H
-
-#include <stdint.h>
-
-static inline uint64_t kbi_popcount64(uint64_t y) // standard popcount; from wikipedia
-{
- y -= ((y >> 1) & 0x5555555555555555ull);
- y = (y & 0x3333333333333333ull) + (y >> 2 & 0x3333333333333333ull);
- return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
-}
-
-static inline uint64_t kbi_DNAcount64(uint64_t y, int c) // count #A/C/G/T from a 2-bit encoded integer; from BWA
-{
- // reduce nucleotide counting to bits counting
- y = ((c&2)? y : ~y) >> 1 & ((c&1)? y : ~y) & 0x5555555555555555ull;
- // count the number of 1s in y
- y = (y & 0x3333333333333333ull) + (y >> 2 & 0x3333333333333333ull);
- return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
-}
-
-#ifndef kroundup32 // round a 32-bit integer to the next closet integer; from "bit twiddling hacks"
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-#ifndef kbi_swap
-#define kbi_swap(a, b) (((a) ^= (b)), ((b) ^= (a)), ((a) ^= (b))) // from "bit twiddling hacks"
-#endif
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kbtree.h b/debian/vendor-h2o/deps/klib/kbtree.h
deleted file mode 100644
index 5ed5330..0000000
--- a/debian/vendor-h2o/deps/klib/kbtree.h
+++ /dev/null
@@ -1,384 +0,0 @@
-/*-
- * Copyright 1997-1999, 2001, John-Mark Gurney.
- * 2008-2009, Attractive Chaos <attractor@live.co.uk>
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *
- * 1. Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in the
- * documentation and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
- * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
- * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
- * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- * SUCH DAMAGE.
- */
-
-#ifndef __AC_KBTREE_H
-#define __AC_KBTREE_H
-
-#include <stdlib.h>
-#include <string.h>
-#include <stdint.h>
-
-typedef struct {
- int32_t is_internal:1, n:31;
-} kbnode_t;
-
-#define __KB_KEY(type, x) ((type*)((char*)x + 4))
-#define __KB_PTR(btr, x) ((kbnode_t**)((char*)x + btr->off_ptr))
-
-#define __KB_TREE_T(name) \
- typedef struct { \
- kbnode_t *root; \
- int off_key, off_ptr, ilen, elen; \
- int n, t; \
- int n_keys, n_nodes; \
- } kbtree_##name##_t;
-
-#define __KB_INIT(name, key_t) \
- kbtree_##name##_t *kb_init_##name(int size) \
- { \
- kbtree_##name##_t *b; \
- b = (kbtree_##name##_t*)calloc(1, sizeof(kbtree_##name##_t)); \
- b->t = ((size - 4 - sizeof(void*)) / (sizeof(void*) + sizeof(key_t)) + 1) >> 1; \
- if (b->t < 2) { \
- free(b); return 0; \
- } \
- b->n = 2 * b->t - 1; \
- b->off_ptr = 4 + b->n * sizeof(key_t); \
- b->ilen = (4 + sizeof(void*) + b->n * (sizeof(void*) + sizeof(key_t)) + 3) >> 2 << 2; \
- b->elen = (b->off_ptr + 3) >> 2 << 2; \
- b->root = (kbnode_t*)calloc(1, b->ilen); \
- ++b->n_nodes; \
- return b; \
- }
-
-#define __kb_destroy(b) do { \
- int i, max = 8; \
- kbnode_t *x, **top, **stack = 0; \
- if (b) { \
- top = stack = (kbnode_t**)calloc(max, sizeof(kbnode_t*)); \
- *top++ = (b)->root; \
- while (top != stack) { \
- x = *--top; \
- if (x->is_internal == 0) { free(x); continue; } \
- for (i = 0; i <= x->n; ++i) \
- if (__KB_PTR(b, x)[i]) { \
- if (top - stack == max) { \
- max <<= 1; \
- stack = (kbnode_t**)realloc(stack, max * sizeof(kbnode_t*)); \
- top = stack + (max>>1); \
- } \
- *top++ = __KB_PTR(b, x)[i]; \
- } \
- free(x); \
- } \
- } \
- free(b); free(stack); \
- } while (0)
-
-#define __kb_get_first(key_t, b, ret) do { \
- kbnode_t *__x = (b)->root; \
- while (__KB_PTR(b, __x)[0] != 0) \
- __x = __KB_PTR(b, __x)[0]; \
- (ret) = __KB_KEY(key_t, __x)[0]; \
- } while (0)
-
-#define __KB_GET_AUX0(name, key_t, __cmp) \
- static inline int __kb_get_aux_##name(const kbnode_t * __restrict x, const key_t * __restrict k, int *r) \
- { \
- int tr, *rr, begin, end, n = x->n >> 1; \
- if (x->n == 0) return -1; \
- if (__cmp(*k, __KB_KEY(key_t, x)[n]) < 0) { \
- begin = 0; end = n; \
- } else { begin = n; end = x->n - 1; } \
- rr = r? r : &tr; \
- n = end; \
- while (n >= begin && (*rr = __cmp(*k, __KB_KEY(key_t, x)[n])) < 0) --n; \
- return n; \
- }
-
-#define __KB_GET_AUX1(name, key_t, __cmp) \
- static inline int __kb_getp_aux_##name(const kbnode_t * __restrict x, const key_t * __restrict k, int *r) \
- { \
- int tr, *rr, begin = 0, end = x->n; \
- if (x->n == 0) return -1; \
- rr = r? r : &tr; \
- while (begin < end) { \
- int mid = (begin + end) >> 1; \
- if (__cmp(__KB_KEY(key_t, x)[mid], *k) < 0) begin = mid + 1; \
- else end = mid; \
- } \
- if (begin == x->n) { *rr = 1; return x->n - 1; } \
- if ((*rr = __cmp(*k, __KB_KEY(key_t, x)[begin])) < 0) --begin; \
- return begin; \
- }
-
-#define __KB_GET(name, key_t) \
- static key_t *kb_getp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
- { \
- int i, r = 0; \
- kbnode_t *x = b->root; \
- while (x) { \
- i = __kb_getp_aux_##name(x, k, &r); \
- if (i >= 0 && r == 0) return &__KB_KEY(key_t, x)[i]; \
- if (x->is_internal == 0) return 0; \
- x = __KB_PTR(b, x)[i + 1]; \
- } \
- return 0; \
- } \
- static inline key_t *kb_get_##name(kbtree_##name##_t *b, const key_t k) \
- { \
- return kb_getp_##name(b, &k); \
- }
-
-#define __KB_INTERVAL(name, key_t) \
- static void kb_intervalp_##name(kbtree_##name##_t *b, const key_t * __restrict k, key_t **lower, key_t **upper) \
- { \
- int i, r = 0; \
- kbnode_t *x = b->root; \
- *lower = *upper = 0; \
- while (x) { \
- i = __kb_getp_aux_##name(x, k, &r); \
- if (i >= 0 && r == 0) { \
- *lower = *upper = &__KB_KEY(key_t, x)[i]; \
- return; \
- } \
- if (i >= 0) *lower = &__KB_KEY(key_t, x)[i]; \
- if (i < x->n - 1) *upper = &__KB_KEY(key_t, x)[i + 1]; \
- if (x->is_internal == 0) return; \
- x = __KB_PTR(b, x)[i + 1]; \
- } \
- } \
- static inline void kb_interval_##name(kbtree_##name##_t *b, const key_t k, key_t **lower, key_t **upper) \
- { \
- kb_intervalp_##name(b, &k, lower, upper); \
- }
-
-#define __KB_PUT(name, key_t, __cmp) \
- /* x must be an internal node */ \
- static void __kb_split_##name(kbtree_##name##_t *b, kbnode_t *x, int i, kbnode_t *y) \
- { \
- kbnode_t *z; \
- z = (kbnode_t*)calloc(1, y->is_internal? b->ilen : b->elen); \
- ++b->n_nodes; \
- z->is_internal = y->is_internal; \
- z->n = b->t - 1; \
- memcpy(__KB_KEY(key_t, z), __KB_KEY(key_t, y) + b->t, sizeof(key_t) * (b->t - 1)); \
- if (y->is_internal) memcpy(__KB_PTR(b, z), __KB_PTR(b, y) + b->t, sizeof(void*) * b->t); \
- y->n = b->t - 1; \
- memmove(__KB_PTR(b, x) + i + 2, __KB_PTR(b, x) + i + 1, sizeof(void*) * (x->n - i)); \
- __KB_PTR(b, x)[i + 1] = z; \
- memmove(__KB_KEY(key_t, x) + i + 1, __KB_KEY(key_t, x) + i, sizeof(key_t) * (x->n - i)); \
- __KB_KEY(key_t, x)[i] = __KB_KEY(key_t, y)[b->t - 1]; \
- ++x->n; \
- } \
- static void __kb_putp_aux_##name(kbtree_##name##_t *b, kbnode_t *x, const key_t * __restrict k) \
- { \
- int i = x->n - 1; \
- if (x->is_internal == 0) { \
- i = __kb_getp_aux_##name(x, k, 0); \
- if (i != x->n - 1) \
- memmove(__KB_KEY(key_t, x) + i + 2, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
- __KB_KEY(key_t, x)[i + 1] = *k; \
- ++x->n; \
- } else { \
- i = __kb_getp_aux_##name(x, k, 0) + 1; \
- if (__KB_PTR(b, x)[i]->n == 2 * b->t - 1) { \
- __kb_split_##name(b, x, i, __KB_PTR(b, x)[i]); \
- if (__cmp(*k, __KB_KEY(key_t, x)[i]) > 0) ++i; \
- } \
- __kb_putp_aux_##name(b, __KB_PTR(b, x)[i], k); \
- } \
- } \
- static void kb_putp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
- { \
- kbnode_t *r, *s; \
- ++b->n_keys; \
- r = b->root; \
- if (r->n == 2 * b->t - 1) { \
- ++b->n_nodes; \
- s = (kbnode_t*)calloc(1, b->ilen); \
- b->root = s; s->is_internal = 1; s->n = 0; \
- __KB_PTR(b, s)[0] = r; \
- __kb_split_##name(b, s, 0, r); \
- r = s; \
- } \
- __kb_putp_aux_##name(b, r, k); \
- } \
- static inline void kb_put_##name(kbtree_##name##_t *b, const key_t k) \
- { \
- kb_putp_##name(b, &k); \
- }
-
-
-#define __KB_DEL(name, key_t) \
- static key_t __kb_delp_aux_##name(kbtree_##name##_t *b, kbnode_t *x, const key_t * __restrict k, int s) \
- { \
- int yn, zn, i, r = 0; \
- kbnode_t *xp, *y, *z; \
- key_t kp; \
- if (x == 0) return *k; \
- if (s) { /* s can only be 0, 1 or 2 */ \
- r = x->is_internal == 0? 0 : s == 1? 1 : -1; \
- i = s == 1? x->n - 1 : -1; \
- } else i = __kb_getp_aux_##name(x, k, &r); \
- if (x->is_internal == 0) { \
- if (s == 2) ++i; \
- kp = __KB_KEY(key_t, x)[i]; \
- memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
- --x->n; \
- return kp; \
- } \
- if (r == 0) { \
- if ((yn = __KB_PTR(b, x)[i]->n) >= b->t) { \
- xp = __KB_PTR(b, x)[i]; \
- kp = __KB_KEY(key_t, x)[i]; \
- __KB_KEY(key_t, x)[i] = __kb_delp_aux_##name(b, xp, 0, 1); \
- return kp; \
- } else if ((zn = __KB_PTR(b, x)[i + 1]->n) >= b->t) { \
- xp = __KB_PTR(b, x)[i + 1]; \
- kp = __KB_KEY(key_t, x)[i]; \
- __KB_KEY(key_t, x)[i] = __kb_delp_aux_##name(b, xp, 0, 2); \
- return kp; \
- } else if (yn == b->t - 1 && zn == b->t - 1) { \
- y = __KB_PTR(b, x)[i]; z = __KB_PTR(b, x)[i + 1]; \
- __KB_KEY(key_t, y)[y->n++] = *k; \
- memmove(__KB_KEY(key_t, y) + y->n, __KB_KEY(key_t, z), z->n * sizeof(key_t)); \
- if (y->is_internal) memmove(__KB_PTR(b, y) + y->n, __KB_PTR(b, z), (z->n + 1) * sizeof(void*)); \
- y->n += z->n; \
- memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
- memmove(__KB_PTR(b, x) + i + 1, __KB_PTR(b, x) + i + 2, (x->n - i - 1) * sizeof(void*)); \
- --x->n; \
- free(z); \
- return __kb_delp_aux_##name(b, y, k, s); \
- } \
- } \
- ++i; \
- if ((xp = __KB_PTR(b, x)[i])->n == b->t - 1) { \
- if (i > 0 && (y = __KB_PTR(b, x)[i - 1])->n >= b->t) { \
- memmove(__KB_KEY(key_t, xp) + 1, __KB_KEY(key_t, xp), xp->n * sizeof(key_t)); \
- if (xp->is_internal) memmove(__KB_PTR(b, xp) + 1, __KB_PTR(b, xp), (xp->n + 1) * sizeof(void*)); \
- __KB_KEY(key_t, xp)[0] = __KB_KEY(key_t, x)[i - 1]; \
- __KB_KEY(key_t, x)[i - 1] = __KB_KEY(key_t, y)[y->n - 1]; \
- if (xp->is_internal) __KB_PTR(b, xp)[0] = __KB_PTR(b, y)[y->n]; \
- --y->n; ++xp->n; \
- } else if (i < x->n && (y = __KB_PTR(b, x)[i + 1])->n >= b->t) { \
- __KB_KEY(key_t, xp)[xp->n++] = __KB_KEY(key_t, x)[i]; \
- __KB_KEY(key_t, x)[i] = __KB_KEY(key_t, y)[0]; \
- if (xp->is_internal) __KB_PTR(b, xp)[xp->n] = __KB_PTR(b, y)[0]; \
- --y->n; \
- memmove(__KB_KEY(key_t, y), __KB_KEY(key_t, y) + 1, y->n * sizeof(key_t)); \
- if (y->is_internal) memmove(__KB_PTR(b, y), __KB_PTR(b, y) + 1, (y->n + 1) * sizeof(void*)); \
- } else if (i > 0 && (y = __KB_PTR(b, x)[i - 1])->n == b->t - 1) { \
- __KB_KEY(key_t, y)[y->n++] = __KB_KEY(key_t, x)[i - 1]; \
- memmove(__KB_KEY(key_t, y) + y->n, __KB_KEY(key_t, xp), xp->n * sizeof(key_t)); \
- if (y->is_internal) memmove(__KB_PTR(b, y) + y->n, __KB_PTR(b, xp), (xp->n + 1) * sizeof(void*)); \
- y->n += xp->n; \
- memmove(__KB_KEY(key_t, x) + i - 1, __KB_KEY(key_t, x) + i, (x->n - i) * sizeof(key_t)); \
- memmove(__KB_PTR(b, x) + i, __KB_PTR(b, x) + i + 1, (x->n - i) * sizeof(void*)); \
- --x->n; \
- free(xp); \
- xp = y; \
- } else if (i < x->n && (y = __KB_PTR(b, x)[i + 1])->n == b->t - 1) { \
- __KB_KEY(key_t, xp)[xp->n++] = __KB_KEY(key_t, x)[i]; \
- memmove(__KB_KEY(key_t, xp) + xp->n, __KB_KEY(key_t, y), y->n * sizeof(key_t)); \
- if (xp->is_internal) memmove(__KB_PTR(b, xp) + xp->n, __KB_PTR(b, y), (y->n + 1) * sizeof(void*)); \
- xp->n += y->n; \
- memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
- memmove(__KB_PTR(b, x) + i + 1, __KB_PTR(b, x) + i + 2, (x->n - i - 1) * sizeof(void*)); \
- --x->n; \
- free(y); \
- } \
- } \
- return __kb_delp_aux_##name(b, xp, k, s); \
- } \
- static key_t kb_delp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
- { \
- kbnode_t *x; \
- key_t ret; \
- ret = __kb_delp_aux_##name(b, b->root, k, 0); \
- --b->n_keys; \
- if (b->root->n == 0 && b->root->is_internal) { \
- --b->n_nodes; \
- x = b->root; \
- b->root = __KB_PTR(b, x)[0]; \
- free(x); \
- } \
- return ret; \
- } \
- static inline key_t kb_del_##name(kbtree_##name##_t *b, const key_t k) \
- { \
- return kb_delp_##name(b, &k); \
- }
-
-typedef struct {
- kbnode_t *x;
- int i;
-} __kbstack_t;
-
-#define __kb_traverse(key_t, b, __func) do { \
- int __kmax = 8; \
- __kbstack_t *__kstack, *__kp; \
- __kp = __kstack = (__kbstack_t*)calloc(__kmax, sizeof(__kbstack_t)); \
- __kp->x = (b)->root; __kp->i = 0; \
- for (;;) { \
- while (__kp->x && __kp->i <= __kp->x->n) { \
- if (__kp - __kstack == __kmax - 1) { \
- __kmax <<= 1; \
- __kstack = (__kbstack_t*)realloc(__kstack, __kmax * sizeof(__kbstack_t)); \
- __kp = __kstack + (__kmax>>1) - 1; \
- } \
- (__kp+1)->i = 0; (__kp+1)->x = __kp->x->is_internal? __KB_PTR(b, __kp->x)[__kp->i] : 0; \
- ++__kp; \
- } \
- --__kp; \
- if (__kp >= __kstack) { \
- if (__kp->x && __kp->i < __kp->x->n) __func(&__KB_KEY(key_t, __kp->x)[__kp->i]); \
- ++__kp->i; \
- } else break; \
- } \
- free(__kstack); \
- } while (0)
-
-#define KBTREE_INIT(name, key_t, __cmp) \
- __KB_TREE_T(name) \
- __KB_INIT(name, key_t) \
- __KB_GET_AUX1(name, key_t, __cmp) \
- __KB_GET(name, key_t) \
- __KB_INTERVAL(name, key_t) \
- __KB_PUT(name, key_t, __cmp) \
- __KB_DEL(name, key_t)
-
-#define KB_DEFAULT_SIZE 512
-
-#define kbtree_t(name) kbtree_##name##_t
-#define kb_init(name, s) kb_init_##name(s)
-#define kb_destroy(name, b) __kb_destroy(b)
-#define kb_get(name, b, k) kb_get_##name(b, k)
-#define kb_put(name, b, k) kb_put_##name(b, k)
-#define kb_del(name, b, k) kb_del_##name(b, k)
-#define kb_interval(name, b, k, l, u) kb_interval_##name(b, k, l, u)
-#define kb_getp(name, b, k) kb_getp_##name(b, k)
-#define kb_putp(name, b, k) kb_putp_##name(b, k)
-#define kb_delp(name, b, k) kb_delp_##name(b, k)
-#define kb_intervalp(name, b, k, l, u) kb_intervalp_##name(b, k, l, u)
-
-#define kb_size(b) ((b)->n_keys)
-
-#define kb_generic_cmp(a, b) (((b) < (a)) - ((a) < (b)))
-#define kb_str_cmp(a, b) strcmp(a, b)
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kgraph.h b/debian/vendor-h2o/deps/klib/kgraph.h
deleted file mode 100644
index af008ef..0000000
--- a/debian/vendor-h2o/deps/klib/kgraph.h
+++ /dev/null
@@ -1,79 +0,0 @@
-#ifndef AC_KGRAPH_H
-#define AC_KGRAPH_H
-
-#include <stdint.h>
-#include <stdlib.h>
-#include "khash.h"
-#include "kbtree.h"
-
-typedef unsigned kgint_t;
-
-#define kgraph_t(name) kh_##name##_t
-
-#define __KG_BASIC(name, SCOPE, vertex_t, arc_t, ehn) \
- SCOPE kgraph_t(name) *kg_init_##name(void) { return kh_init(name); } \
- SCOPE void kg_destroy_##name(kgraph_t(name) *g) { \
- khint_t k; \
- if (g == 0) return; \
- for (k = kh_begin(g); k != kh_end(g); ++k) \
- if (kh_exist(g, k)) kh_destroy(ehn, kh_val(g, k)._arc); \
- kh_destroy(name, g); \
- } \
- SCOPE vertex_t *kg_get_v_##name(kgraph_t(name) *g, kgint_t v) { \
- khint_t k = kh_get(name, g, v); \
- return k == kh_end(g)? 0 : &kh_val(g, k); \
- } \
- SCOPE vertex_t *kg_put_v_##name(kgraph_t(name) *g, kgint_t v, int *absent) { \
- khint_t k; \
- k = kh_put(name, g, v, absent); \
- if (*absent) kh_val(g, k)._arc = kh_init(ehn); \
- return &kh_val(g, k); \
- } \
- SCOPE void kg_put_a_##name(kgraph_t(name) *g, kgint_t vbeg, kgint_t vend, int dir, arc_t **pb, arc_t **pe) { \
- vertex_t *p; \
- khint_t k; \
- int absent; \
- p = kg_put_v_##name(g, vbeg, &absent); \
- k = kh_put(ehn, p->_arc, vend<<2|dir, &absent); \
- *pb = &kh_val(p->_arc, k); \
- p = kg_put_v_##name(g, vend, &absent); \
- k = kh_put(ehn, p->_arc, vbeg<<2|(~dir&3), &absent); \
- *pe = &kh_val(p->_arc, k); \
- } \
- SCOPE vertex_t *kg_del_v_##name(kgraph_t(name) *g, kgint_t v) { \
- khint_t k, k0, k2, k3; \
- khash_t(ehn) *h; \
- k0 = k = kh_get(name, g, v); \
- if (k == kh_end(g)) return 0; /* not present in the graph */ \
- h = kh_val(g, k)._arc; \
- for (k = kh_begin(h); k != kh_end(h); ++k) /* remove v from its neighbors */ \
- if (kh_exist(h, k)) { \
- k2 = kh_get(name, g, kh_key(h, k)>>2); \
- /* assert(k2 != kh_end(g)); */ \
- k3 = kh_get(ehn, kh_val(g, k2)._arc, v<<2|(~kh_key(h, k)&3)); \
- /* assert(k3 != kh_end(kh_val(g, k2)._arc)); */ \
- kh_del(ehn, kh_val(g, k2)._arc, k3); \
- } \
- kh_destroy(ehn, h); \
- kh_del(name, g, k0); \
- return &kh_val(g, k0); \
- }
-
-#define KGRAPH_PRINT(name, SCOPE) \
- SCOPE void kg_print_##name(kgraph_t(name) *g) { \
- khint_t k, k2; \
- for (k = kh_begin(g); k != kh_end(g); ++k) \
- if (kh_exist(g, k)) { \
- printf("v %u\n", kh_key(g, k)); \
- for (k2 = kh_begin(kh_val(g, k)._arc); k2 != kh_end(kh_val(g, k)._arc); ++k2) \
- if (kh_exist(kh_val(g, k)._arc, k2) && kh_key(g, k) < kh_key(kh_val(g, k)._arc, k2)>>2) \
- printf("a %u%c%c%u\n", kh_key(g, k), "><"[kh_key(kh_val(g, k)._arc, k2)>>1&1], \
- "><"[kh_key(kh_val(g, k)._arc, k2)&1], kh_key(kh_val(g, k)._arc, k2)>>2); \
- } \
- }
-
-#define KGRAPH_INIT(name, SCOPE, vertex_t, arc_t, ehn) \
- KHASH_INIT2(name, SCOPE, kgint_t, vertex_t, 1, kh_int_hash_func, kh_int_hash_equal) \
- __KG_BASIC(name, SCOPE, vertex_t, arc_t, ehn)
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/khash.h b/debian/vendor-h2o/deps/klib/khash.h
deleted file mode 100644
index 5e55088..0000000
--- a/debian/vendor-h2o/deps/klib/khash.h
+++ /dev/null
@@ -1,619 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008, 2009, 2011 by Attractive Chaos <attractor@live.co.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.
-*/
-
-/*
- An example:
-
-#include "khash.h"
-KHASH_MAP_INIT_INT(32, char)
-int main() {
- int ret, is_missing;
- khiter_t k;
- khash_t(32) *h = kh_init(32);
- k = kh_put(32, h, 5, &ret);
- kh_value(h, k) = 10;
- k = kh_get(32, h, 10);
- is_missing = (k == kh_end(h));
- k = kh_get(32, h, 5);
- kh_del(32, h, k);
- for (k = kh_begin(h); k != kh_end(h); ++k)
- if (kh_exist(h, k)) kh_value(h, k) = 1;
- kh_destroy(32, h);
- return 0;
-}
-*/
-
-/*
- 2013-05-02 (0.2.8):
-
- * Use quadratic probing. When the capacity is power of 2, stepping function
- i*(i+1)/2 guarantees to traverse each bucket. It is better than double
- hashing on cache performance and is more robust than linear probing.
-
- In theory, double hashing should be more robust than quadratic probing.
- However, my implementation is probably not for large hash tables, because
- the second hash function is closely tied to the first hash function,
- which reduce the effectiveness of double hashing.
-
- Reference: http://research.cs.vt.edu/AVresearch/hashing/quadratic.php
-
- 2011-12-29 (0.2.7):
-
- * Minor code clean up; no actual effect.
-
- 2011-09-16 (0.2.6):
-
- * The capacity is a power of 2. This seems to dramatically improve the
- speed for simple keys. Thank Zilong Tan for the suggestion. Reference:
-
- - http://code.google.com/p/ulib/
- - http://nothings.org/computer/judy/
-
- * Allow to optionally use linear probing which usually has better
- performance for random input. Double hashing is still the default as it
- is more robust to certain non-random input.
-
- * Added Wang's integer hash function (not used by default). This hash
- function is more robust to certain non-random input.
-
- 2011-02-14 (0.2.5):
-
- * Allow to declare global functions.
-
- 2009-09-26 (0.2.4):
-
- * Improve portability
-
- 2008-09-19 (0.2.3):
-
- * Corrected the example
- * Improved interfaces
-
- 2008-09-11 (0.2.2):
-
- * Improved speed a little in kh_put()
-
- 2008-09-10 (0.2.1):
-
- * Added kh_clear()
- * Fixed a compiling error
-
- 2008-09-02 (0.2.0):
-
- * Changed to token concatenation which increases flexibility.
-
- 2008-08-31 (0.1.2):
-
- * Fixed a bug in kh_get(), which has not been tested previously.
-
- 2008-08-31 (0.1.1):
-
- * Added destructor
-*/
-
-
-#ifndef __AC_KHASH_H
-#define __AC_KHASH_H
-
-/*!
- @header
-
- Generic hash table library.
- */
-
-#define AC_VERSION_KHASH_H "0.2.8"
-
-#include <stdlib.h>
-#include <string.h>
-#include <limits.h>
-
-/* compiler specific configuration */
-
-#if UINT_MAX == 0xffffffffu
-typedef unsigned int khint32_t;
-#elif ULONG_MAX == 0xffffffffu
-typedef unsigned long khint32_t;
-#endif
-
-#if ULONG_MAX == ULLONG_MAX
-typedef unsigned long khint64_t;
-#else
-typedef unsigned long long khint64_t;
-#endif
-
-#ifndef kh_inline
-#ifdef _MSC_VER
-#define kh_inline __inline
-#else
-#define kh_inline inline
-#endif
-#endif /* kh_inline */
-
-typedef khint32_t khint_t;
-typedef khint_t khiter_t;
-
-#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
-#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
-#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
-#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
-#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
-#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
-#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))
-
-#define __ac_fsize(m) ((m) < 16? 1 : (m)>>4)
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-#ifndef kcalloc
-#define kcalloc(N,Z) calloc(N,Z)
-#endif
-#ifndef kmalloc
-#define kmalloc(Z) malloc(Z)
-#endif
-#ifndef krealloc
-#define krealloc(P,Z) realloc(P,Z)
-#endif
-#ifndef kfree
-#define kfree(P) free(P)
-#endif
-
-static const double __ac_HASH_UPPER = 0.77;
-
-#define __KHASH_TYPE(name, khkey_t, khval_t) \
- typedef struct kh_##name##_s { \
- khint_t n_buckets, size, n_occupied, upper_bound; \
- khint32_t *flags; \
- khkey_t *keys; \
- khval_t *vals; \
- } kh_##name##_t;
-
-#define __KHASH_PROTOTYPES(name, khkey_t, khval_t) \
- extern kh_##name##_t *kh_init_##name(void); \
- extern void kh_destroy_##name(kh_##name##_t *h); \
- extern void kh_clear_##name(kh_##name##_t *h); \
- extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); \
- extern int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \
- extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \
- extern void kh_del_##name(kh_##name##_t *h, khint_t x);
-
-#define __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
- SCOPE kh_##name##_t *kh_init_##name(void) { \
- return (kh_##name##_t*)kcalloc(1, sizeof(kh_##name##_t)); \
- } \
- SCOPE void kh_destroy_##name(kh_##name##_t *h) \
- { \
- if (h) { \
- kfree((void *)h->keys); kfree(h->flags); \
- kfree((void *)h->vals); \
- kfree(h); \
- } \
- } \
- SCOPE void kh_clear_##name(kh_##name##_t *h) \
- { \
- if (h && h->flags) { \
- memset(h->flags, 0xaa, __ac_fsize(h->n_buckets) * sizeof(khint32_t)); \
- h->size = h->n_occupied = 0; \
- } \
- } \
- SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
- { \
- if (h->n_buckets) { \
- khint_t k, i, last, mask, step = 0; \
- mask = h->n_buckets - 1; \
- k = __hash_func(key); i = k & mask; \
- last = i; \
- while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
- i = (i + (++step)) & mask; \
- if (i == last) return h->n_buckets; \
- } \
- return __ac_iseither(h->flags, i)? h->n_buckets : i; \
- } else return 0; \
- } \
- SCOPE int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
- { /* This function uses 0.25*n_buckets bytes of working space instead of [sizeof(key_t+val_t)+.25]*n_buckets. */ \
- khint32_t *new_flags = 0; \
- khint_t j = 1; \
- { \
- kroundup32(new_n_buckets); \
- if (new_n_buckets < 4) new_n_buckets = 4; \
- if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; /* requested size is too small */ \
- else { /* hash table size to be changed (shrink or expand); rehash */ \
- new_flags = (khint32_t*)kmalloc(__ac_fsize(new_n_buckets) * sizeof(khint32_t)); \
- if (!new_flags) return -1; \
- memset(new_flags, 0xaa, __ac_fsize(new_n_buckets) * sizeof(khint32_t)); \
- if (h->n_buckets < new_n_buckets) { /* expand */ \
- khkey_t *new_keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \
- if (!new_keys) { kfree(new_flags); return -1; } \
- h->keys = new_keys; \
- if (kh_is_map) { \
- khval_t *new_vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \
- if (!new_vals) { kfree(new_flags); return -1; } \
- h->vals = new_vals; \
- } \
- } /* otherwise shrink */ \
- } \
- } \
- if (j) { /* rehashing is needed */ \
- for (j = 0; j != h->n_buckets; ++j) { \
- if (__ac_iseither(h->flags, j) == 0) { \
- khkey_t key = h->keys[j]; \
- khval_t val; \
- khint_t new_mask; \
- new_mask = new_n_buckets - 1; \
- if (kh_is_map) val = h->vals[j]; \
- __ac_set_isdel_true(h->flags, j); \
- while (1) { /* kick-out process; sort of like in Cuckoo hashing */ \
- khint_t k, i, step = 0; \
- k = __hash_func(key); \
- i = k & new_mask; \
- while (!__ac_isempty(new_flags, i)) i = (i + (++step)) & new_mask; \
- __ac_set_isempty_false(new_flags, i); \
- if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { /* kick out the existing element */ \
- { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
- if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
- __ac_set_isdel_true(h->flags, i); /* mark it as deleted in the old hash table */ \
- } else { /* write the element and jump out of the loop */ \
- h->keys[i] = key; \
- if (kh_is_map) h->vals[i] = val; \
- break; \
- } \
- } \
- } \
- } \
- if (h->n_buckets > new_n_buckets) { /* shrink the hash table */ \
- h->keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \
- if (kh_is_map) h->vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \
- } \
- kfree(h->flags); /* free the working space */ \
- h->flags = new_flags; \
- h->n_buckets = new_n_buckets; \
- h->n_occupied = h->size; \
- h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
- } \
- return 0; \
- } \
- SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
- { \
- khint_t x; \
- if (h->n_occupied >= h->upper_bound) { /* update the hash table */ \
- if (h->n_buckets > (h->size<<1)) { \
- if (kh_resize_##name(h, h->n_buckets - 1) < 0) { /* clear "deleted" elements */ \
- *ret = -1; return h->n_buckets; \
- } \
- } else if (kh_resize_##name(h, h->n_buckets + 1) < 0) { /* expand the hash table */ \
- *ret = -1; return h->n_buckets; \
- } \
- } /* TODO: to implement automatically shrinking; resize() already support shrinking */ \
- { \
- khint_t k, i, site, last, mask = h->n_buckets - 1, step = 0; \
- x = site = h->n_buckets; k = __hash_func(key); i = k & mask; \
- if (__ac_isempty(h->flags, i)) x = i; /* for speed up */ \
- else { \
- last = i; \
- while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
- if (__ac_isdel(h->flags, i)) site = i; \
- i = (i + (++step)) & mask; \
- if (i == last) { x = site; break; } \
- } \
- if (x == h->n_buckets) { \
- if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
- else x = i; \
- } \
- } \
- } \
- if (__ac_isempty(h->flags, x)) { /* not present at all */ \
- h->keys[x] = key; \
- __ac_set_isboth_false(h->flags, x); \
- ++h->size; ++h->n_occupied; \
- *ret = 1; \
- } else if (__ac_isdel(h->flags, x)) { /* deleted */ \
- h->keys[x] = key; \
- __ac_set_isboth_false(h->flags, x); \
- ++h->size; \
- *ret = 2; \
- } else *ret = 0; /* Don't touch h->keys[x] if present and not deleted */ \
- return x; \
- } \
- SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
- { \
- if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \
- __ac_set_isdel_true(h->flags, x); \
- --h->size; \
- } \
- }
-
-#define KHASH_DECLARE(name, khkey_t, khval_t) \
- __KHASH_TYPE(name, khkey_t, khval_t) \
- __KHASH_PROTOTYPES(name, khkey_t, khval_t)
-
-#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
- __KHASH_TYPE(name, khkey_t, khval_t) \
- __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
-
-#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
- KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
-
-/* --- BEGIN OF HASH FUNCTIONS --- */
-
-/*! @function
- @abstract Integer hash function
- @param key The integer [khint32_t]
- @return The hash value [khint_t]
- */
-#define kh_int_hash_func(key) (khint32_t)(key)
-/*! @function
- @abstract Integer comparison function
- */
-#define kh_int_hash_equal(a, b) ((a) == (b))
-/*! @function
- @abstract 64-bit integer hash function
- @param key The integer [khint64_t]
- @return The hash value [khint_t]
- */
-#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
-/*! @function
- @abstract 64-bit integer comparison function
- */
-#define kh_int64_hash_equal(a, b) ((a) == (b))
-/*! @function
- @abstract const char* hash function
- @param s Pointer to a null terminated string
- @return The hash value
- */
-static kh_inline khint_t __ac_X31_hash_string(const char *s)
-{
- khint_t h = (khint_t)*s;
- if (h) for (++s ; *s; ++s) h = (h << 5) - h + (khint_t)*s;
- return h;
-}
-/*! @function
- @abstract Another interface to const char* hash function
- @param key Pointer to a null terminated string [const char*]
- @return The hash value [khint_t]
- */
-#define kh_str_hash_func(key) __ac_X31_hash_string(key)
-/*! @function
- @abstract Const char* comparison function
- */
-#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)
-
-static kh_inline khint_t __ac_Wang_hash(khint_t key)
-{
- key += ~(key << 15);
- key ^= (key >> 10);
- key += (key << 3);
- key ^= (key >> 6);
- key += ~(key << 11);
- key ^= (key >> 16);
- return key;
-}
-#define kh_int_hash_func2(k) __ac_Wang_hash((khint_t)key)
-
-/* --- END OF HASH FUNCTIONS --- */
-
-/* Other convenient macros... */
-
-/*!
- @abstract Type of the hash table.
- @param name Name of the hash table [symbol]
- */
-#define khash_t(name) kh_##name##_t
-
-/*! @function
- @abstract Initiate a hash table.
- @param name Name of the hash table [symbol]
- @return Pointer to the hash table [khash_t(name)*]
- */
-#define kh_init(name) kh_init_##name()
-
-/*! @function
- @abstract Destroy a hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- */
-#define kh_destroy(name, h) kh_destroy_##name(h)
-
-/*! @function
- @abstract Reset a hash table without deallocating memory.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- */
-#define kh_clear(name, h) kh_clear_##name(h)
-
-/*! @function
- @abstract Resize a hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- @param s New size [khint_t]
- */
-#define kh_resize(name, h, s) kh_resize_##name(h, s)
-
-/*! @function
- @abstract Insert a key to the hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- @param k Key [type of keys]
- @param r Extra return code: -1 if the operation failed;
- 0 if the key is present in the hash table;
- 1 if the bucket is empty (never used); 2 if the element in
- the bucket has been deleted [int*]
- @return Iterator to the inserted element [khint_t]
- */
-#define kh_put(name, h, k, r) kh_put_##name(h, k, r)
-
-/*! @function
- @abstract Retrieve a key from the hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- @param k Key [type of keys]
- @return Iterator to the found element, or kh_end(h) if the element is absent [khint_t]
- */
-#define kh_get(name, h, k) kh_get_##name(h, k)
-
-/*! @function
- @abstract Remove a key from the hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- @param k Iterator to the element to be deleted [khint_t]
- */
-#define kh_del(name, h, k) kh_del_##name(h, k)
-
-/*! @function
- @abstract Test whether a bucket contains data.
- @param h Pointer to the hash table [khash_t(name)*]
- @param x Iterator to the bucket [khint_t]
- @return 1 if containing data; 0 otherwise [int]
- */
-#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))
-
-/*! @function
- @abstract Get key given an iterator
- @param h Pointer to the hash table [khash_t(name)*]
- @param x Iterator to the bucket [khint_t]
- @return Key [type of keys]
- */
-#define kh_key(h, x) ((h)->keys[x])
-
-/*! @function
- @abstract Get value given an iterator
- @param h Pointer to the hash table [khash_t(name)*]
- @param x Iterator to the bucket [khint_t]
- @return Value [type of values]
- @discussion For hash sets, calling this results in segfault.
- */
-#define kh_val(h, x) ((h)->vals[x])
-
-/*! @function
- @abstract Alias of kh_val()
- */
-#define kh_value(h, x) ((h)->vals[x])
-
-/*! @function
- @abstract Get the start iterator
- @param h Pointer to the hash table [khash_t(name)*]
- @return The start iterator [khint_t]
- */
-#define kh_begin(h) (khint_t)(0)
-
-/*! @function
- @abstract Get the end iterator
- @param h Pointer to the hash table [khash_t(name)*]
- @return The end iterator [khint_t]
- */
-#define kh_end(h) ((h)->n_buckets)
-
-/*! @function
- @abstract Get the number of elements in the hash table
- @param h Pointer to the hash table [khash_t(name)*]
- @return Number of elements in the hash table [khint_t]
- */
-#define kh_size(h) ((h)->size)
-
-/*! @function
- @abstract Get the number of buckets in the hash table
- @param h Pointer to the hash table [khash_t(name)*]
- @return Number of buckets in the hash table [khint_t]
- */
-#define kh_n_buckets(h) ((h)->n_buckets)
-
-/*! @function
- @abstract Iterate over the entries in the hash table
- @param h Pointer to the hash table [khash_t(name)*]
- @param kvar Variable to which key will be assigned
- @param vvar Variable to which value will be assigned
- @param code Block of code to execute
- */
-#define kh_foreach(h, kvar, vvar, code) { khint_t __i; \
- for (__i = kh_begin(h); __i != kh_end(h); ++__i) { \
- if (!kh_exist(h,__i)) continue; \
- (kvar) = kh_key(h,__i); \
- (vvar) = kh_val(h,__i); \
- code; \
- } }
-
-/*! @function
- @abstract Iterate over the values in the hash table
- @param h Pointer to the hash table [khash_t(name)*]
- @param vvar Variable to which value will be assigned
- @param code Block of code to execute
- */
-#define kh_foreach_value(h, vvar, code) { khint_t __i; \
- for (__i = kh_begin(h); __i != kh_end(h); ++__i) { \
- if (!kh_exist(h,__i)) continue; \
- (vvar) = kh_val(h,__i); \
- code; \
- } }
-
-/* More conenient interfaces */
-
-/*! @function
- @abstract Instantiate a hash set containing integer keys
- @param name Name of the hash table [symbol]
- */
-#define KHASH_SET_INIT_INT(name) \
- KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
-
-/*! @function
- @abstract Instantiate a hash map containing integer keys
- @param name Name of the hash table [symbol]
- @param khval_t Type of values [type]
- */
-#define KHASH_MAP_INIT_INT(name, khval_t) \
- KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
-
-/*! @function
- @abstract Instantiate a hash map containing 64-bit integer keys
- @param name Name of the hash table [symbol]
- */
-#define KHASH_SET_INIT_INT64(name) \
- KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
-
-/*! @function
- @abstract Instantiate a hash map containing 64-bit integer keys
- @param name Name of the hash table [symbol]
- @param khval_t Type of values [type]
- */
-#define KHASH_MAP_INIT_INT64(name, khval_t) \
- KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
-
-typedef const char *kh_cstr_t;
-/*! @function
- @abstract Instantiate a hash map containing const char* keys
- @param name Name of the hash table [symbol]
- */
-#define KHASH_SET_INIT_STR(name) \
- KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
-
-/*! @function
- @abstract Instantiate a hash map containing const char* keys
- @param name Name of the hash table [symbol]
- @param khval_t Type of values [type]
- */
-#define KHASH_MAP_INIT_STR(name, khval_t) \
- KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
-
-#endif /* __AC_KHASH_H */
diff --git a/debian/vendor-h2o/deps/klib/khmm.c b/debian/vendor-h2o/deps/klib/khmm.c
deleted file mode 100644
index 711ade5..0000000
--- a/debian/vendor-h2o/deps/klib/khmm.c
+++ /dev/null
@@ -1,423 +0,0 @@
-#include <math.h>
-#include <stdio.h>
-#include <assert.h>
-#include <string.h>
-#include <stdlib.h>
-#include "khmm.h"
-
-// new/delete hmm_par_t
-
-hmm_par_t *hmm_new_par(int m, int n)
-{
- hmm_par_t *hp;
- int i;
- assert(m > 0 && n > 0);
- hp = (hmm_par_t*)calloc(1, sizeof(hmm_par_t));
- hp->m = m; hp->n = n;
- hp->a0 = (FLOAT*)calloc(n, sizeof(FLOAT));
- hp->a = (FLOAT**)calloc2(n, n, sizeof(FLOAT));
- hp->e = (FLOAT**)calloc2(m + 1, n, sizeof(FLOAT));
- hp->ae = (FLOAT**)calloc2((m + 1) * n, n, sizeof(FLOAT));
- for (i = 0; i != n; ++i) hp->e[m][i] = 1.0;
- return hp;
-}
-void hmm_delete_par(hmm_par_t *hp)
-{
- int i;
- if (hp == 0) return;
- for (i = 0; i != hp->n; ++i) free(hp->a[i]);
- for (i = 0; i <= hp->m; ++i) free(hp->e[i]);
- for (i = 0; i < (hp->m + 1) * hp->n; ++i) free(hp->ae[i]);
- free(hp->a); free(hp->e); free(hp->a0); free(hp->ae);
- free(hp);
-}
-
-// new/delete hmm_data_t
-
-hmm_data_t *hmm_new_data(int L, const char *seq, const hmm_par_t *hp)
-{
- hmm_data_t *hd;
- hd = (hmm_data_t*)calloc(1, sizeof(hmm_data_t));
- hd->L = L;
- hd->seq = (char*)malloc(L + 1);
- memcpy(hd->seq + 1, seq, L);
- return hd;
-}
-void hmm_delete_data(hmm_data_t *hd)
-{
- int i;
- if (hd == 0) return;
- for (i = 0; i <= hd->L; ++i) {
- if (hd->f) free(hd->f[i]);
- if (hd->b) free(hd->b[i]);
- }
- free(hd->f); free(hd->b); free(hd->s); free(hd->v); free(hd->p); free(hd->seq);
- free(hd);
-}
-
-// new/delete hmm_exp_t
-
-hmm_exp_t *hmm_new_exp(const hmm_par_t *hp)
-{
- hmm_exp_t *he;
- assert(hp);
- he = (hmm_exp_t*)calloc(1, sizeof(hmm_exp_t));
- he->m = hp->m; he->n = hp->n;
- he->A0 = (FLOAT*)calloc(hp->n, sizeof(FLOAT));
- he->A = (FLOAT**)calloc2(hp->n, hp->n, sizeof(FLOAT));
- he->E = (FLOAT**)calloc2(hp->m + 1, hp->n, sizeof(FLOAT));
- return he;
-}
-void hmm_delete_exp(hmm_exp_t *he)
-{
- int i;
- if (he == 0) return;
- for (i = 0; i != he->n; ++i) free(he->A[i]);
- for (i = 0; i <= he->m; ++i) free(he->E[i]);
- free(he->A); free(he->E); free(he->A0);
- free(he);
-}
-
-// Viterbi algorithm
-
-FLOAT hmm_Viterbi(const hmm_par_t *hp, hmm_data_t *hd)
-{
- FLOAT **la, **le, *preV, *curV, max;
- int **Vmax, max_l; // backtrace matrix
- int k, l, b, u;
-
- if (hd->v) free(hd->v);
- hd->v = (int*)calloc(hd->L+1, sizeof(int));
- la = (FLOAT**)calloc2(hp->n, hp->n, sizeof(FLOAT));
- le = (FLOAT**)calloc2(hp->m + 1, hp->n, sizeof(FLOAT));
- Vmax = (int**)calloc2(hd->L+1, hp->n, sizeof(int));
- preV = (FLOAT*)malloc(sizeof(FLOAT) * hp->n);
- curV = (FLOAT*)malloc(sizeof(FLOAT) * hp->n);
- for (k = 0; k != hp->n; ++k)
- for (l = 0; l != hp->n; ++l)
- la[k][l] = log(hp->a[l][k]); // this is not a bug
- for (b = 0; b != hp->m; ++b)
- for (k = 0; k != hp->n; ++k)
- le[b][k] = log(hp->e[b][k]);
- for (k = 0; k != hp->n; ++k) le[hp->m][k] = 0.0;
- // V_k(1)
- for (k = 0; k != hp->n; ++k) {
- preV[k] = le[(int)hd->seq[1]][k] + log(hp->a0[k]);
- Vmax[1][k] = 0;
- }
- // all the rest
- for (u = 2; u <= hd->L; ++u) {
- FLOAT *tmp, *leu = le[(int)hd->seq[u]];
- for (k = 0; k != hp->n; ++k) {
- FLOAT *laa = la[k];
- for (l = 0, max = -HMM_INF, max_l = -1; l != hp->n; ++l) {
- if (max < preV[l] + laa[l]) {
- max = preV[l] + laa[l];
- max_l = l;
- }
- }
- assert(max_l >= 0); // cannot be zero
- curV[k] = leu[k] + max;
- Vmax[u][k] = max_l;
- }
- tmp = curV; curV = preV; preV = tmp; // swap
- }
- // backtrace
- for (k = 0, max_l = -1, max = -HMM_INF; k != hp->n; ++k) {
- if (max < preV[k]) {
- max = preV[k]; max_l = k;
- }
- }
- assert(max_l >= 0); // cannot be zero
- hd->v[hd->L] = max_l;
- for (u = hd->L; u >= 1; --u)
- hd->v[u-1] = Vmax[u][hd->v[u]];
- for (k = 0; k != hp->n; ++k) free(la[k]);
- for (b = 0; b < hp->m; ++b) free(le[b]);
- for (u = 0; u <= hd->L; ++u) free(Vmax[u]);
- free(la); free(le); free(Vmax); free(preV); free(curV);
- hd->status |= HMM_VITERBI;
- return max;
-}
-
-// forward algorithm
-
-void hmm_forward(const hmm_par_t *hp, hmm_data_t *hd)
-{
- FLOAT sum, tmp, **at;
- int u, k, l;
- int n, m, L;
- assert(hp && hd);
- // allocate memory for hd->f and hd->s
- n = hp->n; m = hp->m; L = hd->L;
- if (hd->s) free(hd->s);
- if (hd->f) {
- for (k = 0; k <= hd->L; ++k) free(hd->f[k]);
- free(hd->f);
- }
- hd->f = (FLOAT**)calloc2(hd->L+1, hp->n, sizeof(FLOAT));
- hd->s = (FLOAT*)calloc(hd->L+1, sizeof(FLOAT));
- hd->status &= ~(unsigned)HMM_FORWARD;
- // at[][] array helps to improve the cache efficiency
- at = (FLOAT**)calloc2(n, n, sizeof(FLOAT));
- // transpose a[][]
- for (k = 0; k != n; ++k)
- for (l = 0; l != n; ++l)
- at[k][l] = hp->a[l][k];
- // f[0], but it should never be used
- hd->s[0] = 1.0;
- for (k = 0; k != n; ++k) hd->f[0][k] = 0.0;
- // f[1]
- for (k = 0, sum = 0.0; k != n; ++k)
- sum += (hd->f[1][k] = hp->a0[k] * hp->e[(int)hd->seq[1]][k]);
- for (k = 0; k != n; ++k) hd->f[1][k] /= sum;
- hd->s[1] = sum;
- // f[2..hmmL], the core loop
- for (u = 2; u <= L; ++u) {
- FLOAT *fu = hd->f[u], *fu1 = hd->f[u-1], *eu = hp->e[(int)hd->seq[u]];
- for (k = 0, sum = 0.0; k != n; ++k) {
- FLOAT *aa = at[k];
- for (l = 0, tmp = 0.0; l != n; ++l) tmp += fu1[l] * aa[l];
- sum += (fu[k] = eu[k] * tmp);
- }
- for (k = 0; k != n; ++k) fu[k] /= sum;
- hd->s[u] = sum;
- }
- // free at array
- for (k = 0; k != hp->n; ++k) free(at[k]);
- free(at);
- hd->status |= HMM_FORWARD;
-}
-
-// precalculate hp->ae
-
-void hmm_pre_backward(hmm_par_t *hp)
-{
- int m, n, b, k, l;
- assert(hp);
- m = hp->m; n = hp->n;
- for (b = 0; b <= m; ++b) {
- for (k = 0; k != n; ++k) {
- FLOAT *p = hp->ae[b * hp->n + k];
- for (l = 0; l != n; ++l)
- p[l] = hp->e[b][l] * hp->a[k][l];
- }
- }
-}
-
-// backward algorithm
-
-void hmm_backward(const hmm_par_t *hp, hmm_data_t *hd)
-{
- FLOAT tmp;
- int k, l, u;
- int m, n, L;
- assert(hp && hd);
- assert(hd->status & HMM_FORWARD);
- // allocate memory for hd->b
- m = hp->m; n = hp->n; L = hd->L;
- if (hd->b) {
- for (k = 0; k <= hd->L; ++k) free(hd->b[k]);
- free(hd->b);
- }
- hd->status &= ~(unsigned)HMM_BACKWARD;
- hd->b = (FLOAT**)calloc2(L+1, hp->n, sizeof(FLOAT));
- // b[L]
- for (k = 0; k != hp->n; ++k) hd->b[L][k] = 1.0 / hd->s[L];
- // b[1..L-1], the core loop
- for (u = L-1; u >= 1; --u) {
- FLOAT *bu1 = hd->b[u+1], **p = hp->ae + (int)hd->seq[u+1] * n;
- for (k = 0; k != n; ++k) {
- FLOAT *q = p[k];
- for (l = 0, tmp = 0.0; l != n; ++l) tmp += q[l] * bu1[l];
- hd->b[u][k] = tmp / hd->s[u];
- }
- }
- hd->status |= HMM_BACKWARD;
- for (l = 0, tmp = 0.0; l != n; ++l)
- tmp += hp->a0[l] * hd->b[1][l] * hp->e[(int)hd->seq[1]][l];
- if (tmp > 1.0 + 1e-6 || tmp < 1.0 - 1e-6) // in theory, tmp should always equal to 1
- fprintf(stderr, "++ Underflow may have happened (%lg).\n", tmp);
-}
-
-// log-likelihood of the observation
-
-FLOAT hmm_lk(const hmm_data_t *hd)
-{
- FLOAT sum = 0.0, prod = 1.0;
- int u, L;
- L = hd->L;
- assert(hd->status & HMM_FORWARD);
- for (u = 1; u <= L; ++u) {
- prod *= hd->s[u];
- if (prod < HMM_TINY || prod >= 1.0/HMM_TINY) { // reset
- sum += log(prod);
- prod = 1.0;
- }
- }
- sum += log(prod);
- return sum;
-}
-
-// posterior decoding
-
-void hmm_post_decode(const hmm_par_t *hp, hmm_data_t *hd)
-{
- int u, k;
- assert(hd->status && HMM_BACKWARD);
- if (hd->p) free(hd->p);
- hd->p = (int*)calloc(hd->L + 1, sizeof(int));
- for (u = 1; u <= hd->L; ++u) {
- FLOAT prob, max, *fu = hd->f[u], *bu = hd->b[u], su = hd->s[u];
- int max_k;
- for (k = 0, max = -1.0, max_k = -1; k != hp->n; ++k) {
- if (max < (prob = fu[k] * bu[k] * su)) {
- max = prob; max_k = k;
- }
- }
- assert(max_k >= 0);
- hd->p[u] = max_k;
- }
- hd->status |= HMM_POSTDEC;
-}
-
-// posterior probability of states
-
-FLOAT hmm_post_state(const hmm_par_t *hp, const hmm_data_t *hd, int u, FLOAT *prob)
-{
- FLOAT sum = 0.0, ss = hd->s[u], *fu = hd->f[u], *bu = hd->b[u];
- int k;
- for (k = 0; k != hp->n; ++k)
- sum += (prob[k] = fu[k] * bu[k] * ss);
- return sum; // in theory, this should always equal to 1.0
-}
-
-// expected counts
-
-hmm_exp_t *hmm_expect(const hmm_par_t *hp, const hmm_data_t *hd)
-{
- int k, l, u, b, m, n;
- hmm_exp_t *he;
- assert(hd->status & HMM_BACKWARD);
- he = hmm_new_exp(hp);
- // initialization
- m = hp->m; n = hp->n;
- for (k = 0; k != n; ++k)
- for (l = 0; l != n; ++l) he->A[k][l] = HMM_TINY;
- for (b = 0; b <= m; ++b)
- for (l = 0; l != n; ++l) he->E[b][l] = HMM_TINY;
- // calculate A_{kl} and E_k(b), k,l\in[0,n)
- for (u = 1; u < hd->L; ++u) {
- FLOAT *fu = hd->f[u], *bu = hd->b[u], *bu1 = hd->b[u+1], ss = hd->s[u];
- FLOAT *Ec = he->E[(int)hd->seq[u]], **p = hp->ae + (int)hd->seq[u+1] * n;
- for (k = 0; k != n; ++k) {
- FLOAT *q = p[k], *AA = he->A[k], fuk = fu[k];
- for (l = 0; l != n; ++l) // this is cache-efficient
- AA[l] += fuk * q[l] * bu1[l];
- Ec[k] += fuk * bu[k] * ss;
- }
- }
- // calculate A0_l
- for (l = 0; l != n; ++l)
- he->A0[l] += hp->a0[l] * hp->e[(int)hd->seq[1]][l] * hd->b[1][l];
- return he;
-}
-
-FLOAT hmm_Q0(const hmm_par_t *hp, hmm_exp_t *he)
-{
- int k, l, b;
- FLOAT sum = 0.0;
- for (k = 0; k != hp->n; ++k) {
- FLOAT tmp;
- for (b = 0, tmp = 0.0; b != hp->m; ++b) tmp += he->E[b][k];
- for (b = 0; b != hp->m; ++b)
- sum += he->E[b][k] * log(he->E[b][k] / tmp);
- }
- for (k = 0; k != hp->n; ++k) {
- FLOAT tmp, *A = he->A[k];
- for (l = 0, tmp = 0.0; l != hp->n; ++l) tmp += A[l];
- for (l = 0; l != hp->n; ++l) sum += A[l] * log(A[l] / tmp);
- }
- return (he->Q0 = sum);
-}
-
-// add he0 to he1
-
-void hmm_add_expect(const hmm_exp_t *he0, hmm_exp_t *he1)
-{
- int b, k, l;
- assert(he0->m == he1->m && he0->n == he1->n);
- for (k = 0; k != he1->n; ++k) {
- he1->A0[k] += he0->A0[k];
- for (l = 0; l != he1->n; ++l)
- he1->A[k][l] += he0->A[k][l];
- }
- for (b = 0; b != he1->m; ++b) {
- for (l = 0; l != he1->n; ++l)
- he1->E[b][l] += he0->E[b][l];
- }
-}
-
-// the EM-Q function
-
-FLOAT hmm_Q(const hmm_par_t *hp, const hmm_exp_t *he)
-{
- FLOAT sum = 0.0;
- int bb, k, l;
- for (bb = 0; bb != he->m; ++bb) {
- FLOAT *eb = hp->e[bb], *Eb = he->E[bb];
- for (k = 0; k != hp->n; ++k) {
- if (eb[k] <= 0.0) return -HMM_INF;
- sum += Eb[k] * log(eb[k]);
- }
- }
- for (k = 0; k != he->n; ++k) {
- FLOAT *Ak = he->A[k], *ak = hp->a[k];
- for (l = 0; l != he->n; ++l) {
- if (ak[l] <= 0.0) return -HMM_INF;
- sum += Ak[l] * log(ak[l]);
- }
- }
- return (sum -= he->Q0);
-}
-
-// simulate sequence
-
-char *hmm_simulate(const hmm_par_t *hp, int L)
-{
- int i, k, l, b;
- FLOAT x, y, **et;
- char *seq;
- seq = (char*)calloc(L+1, 1);
- // calculate the transpose of hp->e[][]
- et = (FLOAT**)calloc2(hp->n, hp->m, sizeof(FLOAT));
- for (k = 0; k != hp->n; ++k)
- for (b = 0; b != hp->m; ++b)
- et[k][b] = hp->e[b][k];
- // the initial state, drawn from a0[]
- x = drand48();
- for (k = 0, y = 0.0; k != hp->n; ++k) {
- y += hp->a0[k];
- if (y >= x) break;
- }
- // main loop
- for (i = 0; i != L; ++i) {
- FLOAT *el, *ak = hp->a[k];
- x = drand48();
- for (l = 0, y = 0.0; l != hp->n; ++l) {
- y += ak[l];
- if (y >= x) break;
- }
- el = et[l];
- x = drand48();
- for (b = 0, y = 0.0; b != hp->m; ++b) {
- y += el[b];
- if (y >= x) break;
- }
- seq[i] = b;
- k = l;
- }
- for (k = 0; k != hp->n; ++k) free(et[k]);
- free(et);
- return seq;
-}
diff --git a/debian/vendor-h2o/deps/klib/khmm.h b/debian/vendor-h2o/deps/klib/khmm.h
deleted file mode 100644
index d87673b..0000000
--- a/debian/vendor-h2o/deps/klib/khmm.h
+++ /dev/null
@@ -1,107 +0,0 @@
-#ifndef AC_SCHMM_H_
-#define AC_SCHMM_H_
-
-/*
- * Last Modified: 2008-03-10
- * Version: 0.1.0-8
- *
- * 2008-03-10, 0.1.0-8: make icc report two more "VECTORIZED"
- * 2008-03-10, 0.1.0-7: accelerate for some CPU
- * 2008-02-07, 0.1.0-6: simulate sequences
- * 2008-01-15, 0.1.0-5: goodness of fit
- * 2007-11-20, 0.1.0-4: add function declaration of hmm_post_decode()
- * 2007-11-09: fix a memory leak
- */
-
-#include <stdlib.h>
-
-#define HMM_VERSION "0.1.0-7"
-
-#define HMM_FORWARD 0x02
-#define HMM_BACKWARD 0x04
-#define HMM_VITERBI 0x40
-#define HMM_POSTDEC 0x80
-
-#ifndef FLOAT
-#define FLOAT double
-#endif
-#define HMM_TINY 1e-25
-#define HMM_INF 1e300
-
-typedef struct
-{
- int m, n; // number of symbols, number of states
- FLOAT **a, **e; // transition matrix and emitting probilities
- FLOAT **ae; // auxiliary array for acceleration, should be calculated by hmm_pre_backward()
- FLOAT *a0; // trasition matrix from the start state
-} hmm_par_t;
-
-typedef struct
-{
- int L;
- unsigned status;
- char *seq;
- FLOAT **f, **b, *s;
- int *v; // Viterbi path
- int *p; // posterior decoding
-} hmm_data_t;
-
-typedef struct
-{
- int m, n;
- FLOAT Q0, **A, **E, *A0;
-} hmm_exp_t;
-
-typedef struct
-{
- int l, *obs;
- FLOAT *thr;
-} hmm_gof_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
- /* initialize and destroy hmm_par_t */
- hmm_par_t *hmm_new_par(int m, int n);
- void hmm_delete_par(hmm_par_t *hp);
- /* initialize and destroy hmm_data_t */
- hmm_data_t *hmm_new_data(int L, const char *seq, const hmm_par_t *hp);
- void hmm_delete_data(hmm_data_t *hd);
- /* initialize and destroy hmm_exp_t */
- hmm_exp_t *hmm_new_exp(const hmm_par_t *hp);
- void hmm_delete_exp(hmm_exp_t *he);
- /* Viterbi, forward and backward algorithms */
- FLOAT hmm_Viterbi(const hmm_par_t *hp, hmm_data_t *hd);
- void hmm_pre_backward(hmm_par_t *hp);
- void hmm_forward(const hmm_par_t *hp, hmm_data_t *hd);
- void hmm_backward(const hmm_par_t *hp, hmm_data_t *hd);
- /* log-likelihood of the observations (natural based) */
- FLOAT hmm_lk(const hmm_data_t *hd);
- /* posterior probability at the position on the sequence */
- FLOAT hmm_post_state(const hmm_par_t *hp, const hmm_data_t *hd, int u, FLOAT *prob);
- /* posterior decoding */
- void hmm_post_decode(const hmm_par_t *hp, hmm_data_t *hd);
- /* expected counts of transitions and emissions */
- hmm_exp_t *hmm_expect(const hmm_par_t *hp, const hmm_data_t *hd);
- /* add he0 counts to he1 counts*/
- void hmm_add_expect(const hmm_exp_t *he0, hmm_exp_t *he1);
- /* the Q function that should be maximized in EM */
- FLOAT hmm_Q(const hmm_par_t *hp, const hmm_exp_t *he);
- FLOAT hmm_Q0(const hmm_par_t *hp, hmm_exp_t *he);
- /* simulate sequences */
- char *hmm_simulate(const hmm_par_t *hp, int L);
-#ifdef __cplusplus
-}
-#endif
-
-static inline void **calloc2(int n_row, int n_col, int size)
-{
- char **p;
- int k;
- p = (char**)malloc(sizeof(char*) * n_row);
- for (k = 0; k != n_row; ++k)
- p[k] = (char*)calloc(n_col, size);
- return (void**)p;
-}
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/klist.h b/debian/vendor-h2o/deps/klib/klist.h
deleted file mode 100644
index 8b33f27..0000000
--- a/debian/vendor-h2o/deps/klib/klist.h
+++ /dev/null
@@ -1,121 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008-2009, by Attractive Chaos <attractor@live.co.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 _AC_KLIST_H
-#define _AC_KLIST_H
-
-#include <stdlib.h>
-
-#define KMEMPOOL_INIT(name, kmptype_t, kmpfree_f) \
- typedef struct { \
- size_t cnt, n, max; \
- kmptype_t **buf; \
- } kmp_##name##_t; \
- static inline kmp_##name##_t *kmp_init_##name(void) { \
- return calloc(1, sizeof(kmp_##name##_t)); \
- } \
- static inline void kmp_destroy_##name(kmp_##name##_t *mp) { \
- size_t k; \
- for (k = 0; k < mp->n; ++k) { \
- kmpfree_f(mp->buf[k]); free(mp->buf[k]); \
- } \
- free(mp->buf); free(mp); \
- } \
- static inline kmptype_t *kmp_alloc_##name(kmp_##name##_t *mp) { \
- ++mp->cnt; \
- if (mp->n == 0) return calloc(1, sizeof(kmptype_t)); \
- return mp->buf[--mp->n]; \
- } \
- static inline void kmp_free_##name(kmp_##name##_t *mp, kmptype_t *p) { \
- --mp->cnt; \
- if (mp->n == mp->max) { \
- mp->max = mp->max? mp->max<<1 : 16; \
- mp->buf = realloc(mp->buf, sizeof(kmptype_t *) * mp->max); \
- } \
- mp->buf[mp->n++] = p; \
- }
-
-#define kmempool_t(name) kmp_##name##_t
-#define kmp_init(name) kmp_init_##name()
-#define kmp_destroy(name, mp) kmp_destroy_##name(mp)
-#define kmp_alloc(name, mp) kmp_alloc_##name(mp)
-#define kmp_free(name, mp, p) kmp_free_##name(mp, p)
-
-#define KLIST_INIT(name, kltype_t, kmpfree_t) \
- struct __kl1_##name { \
- kltype_t data; \
- struct __kl1_##name *next; \
- }; \
- typedef struct __kl1_##name kl1_##name; \
- KMEMPOOL_INIT(name, kl1_##name, kmpfree_t) \
- typedef struct { \
- kl1_##name *head, *tail; \
- kmp_##name##_t *mp; \
- size_t size; \
- } kl_##name##_t; \
- static inline kl_##name##_t *kl_init_##name(void) { \
- kl_##name##_t *kl = calloc(1, sizeof(kl_##name##_t)); \
- kl->mp = kmp_init(name); \
- kl->head = kl->tail = kmp_alloc(name, kl->mp); \
- kl->head->next = 0; \
- return kl; \
- } \
- static inline void kl_destroy_##name(kl_##name##_t *kl) { \
- kl1_##name *p; \
- for (p = kl->head; p != kl->tail; p = p->next) \
- kmp_free(name, kl->mp, p); \
- kmp_free(name, kl->mp, p); \
- kmp_destroy(name, kl->mp); \
- free(kl); \
- } \
- static inline kltype_t *kl_pushp_##name(kl_##name##_t *kl) { \
- kl1_##name *q, *p = kmp_alloc(name, kl->mp); \
- q = kl->tail; p->next = 0; kl->tail->next = p; kl->tail = p; \
- ++kl->size; \
- return &q->data; \
- } \
- static inline int kl_shift_##name(kl_##name##_t *kl, kltype_t *d) { \
- kl1_##name *p; \
- if (kl->head->next == 0) return -1; \
- --kl->size; \
- p = kl->head; kl->head = kl->head->next; \
- if (d) *d = p->data; \
- kmp_free(name, kl->mp, p); \
- return 0; \
- }
-
-#define kliter_t(name) kl1_##name
-#define klist_t(name) kl_##name##_t
-#define kl_val(iter) ((iter)->data)
-#define kl_next(iter) ((iter)->next)
-#define kl_begin(kl) ((kl)->head)
-#define kl_end(kl) ((kl)->tail)
-
-#define kl_init(name) kl_init_##name()
-#define kl_destroy(name, kl) kl_destroy_##name(kl)
-#define kl_pushp(name, kl) kl_pushp_##name(kl)
-#define kl_shift(name, kl, d) kl_shift_##name(kl, d)
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kmath.c b/debian/vendor-h2o/deps/klib/kmath.c
deleted file mode 100644
index 9807b00..0000000
--- a/debian/vendor-h2o/deps/klib/kmath.c
+++ /dev/null
@@ -1,456 +0,0 @@
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include "kmath.h"
-
-/**************************************
- *** Pseudo-random number generator ***
- **************************************/
-
-/*
- 64-bit Mersenne Twister pseudorandom number generator. Adapted from:
-
- http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/VERSIONS/C-LANG/mt19937-64.c
-
- which was written by Takuji Nishimura and Makoto Matsumoto and released
- under the 3-clause BSD license.
-*/
-
-#define KR_NN 312
-#define KR_MM 156
-#define KR_UM 0xFFFFFFFF80000000ULL /* Most significant 33 bits */
-#define KR_LM 0x7FFFFFFFULL /* Least significant 31 bits */
-
-struct _krand_t {
- int mti;
- krint64_t mt[KR_NN];
-};
-
-static void kr_srand0(krint64_t seed, krand_t *kr)
-{
- kr->mt[0] = seed;
- for (kr->mti = 1; kr->mti < KR_NN; ++kr->mti)
- kr->mt[kr->mti] = 6364136223846793005ULL * (kr->mt[kr->mti - 1] ^ (kr->mt[kr->mti - 1] >> 62)) + kr->mti;
-}
-
-krand_t *kr_srand(krint64_t seed)
-{
- krand_t *kr;
- kr = malloc(sizeof(krand_t));
- kr_srand0(seed, kr);
- return kr;
-}
-
-krint64_t kr_rand(krand_t *kr)
-{
- krint64_t x;
- static const krint64_t mag01[2] = { 0, 0xB5026F5AA96619E9ULL };
- if (kr->mti >= KR_NN) {
- int i;
- if (kr->mti == KR_NN + 1) kr_srand0(5489ULL, kr);
- for (i = 0; i < KR_NN - KR_MM; ++i) {
- x = (kr->mt[i] & KR_UM) | (kr->mt[i+1] & KR_LM);
- kr->mt[i] = kr->mt[i + KR_MM] ^ (x>>1) ^ mag01[(int)(x&1)];
- }
- for (; i < KR_NN - 1; ++i) {
- x = (kr->mt[i] & KR_UM) | (kr->mt[i+1] & KR_LM);
- kr->mt[i] = kr->mt[i + (KR_MM - KR_NN)] ^ (x>>1) ^ mag01[(int)(x&1)];
- }
- x = (kr->mt[KR_NN - 1] & KR_UM) | (kr->mt[0] & KR_LM);
- kr->mt[KR_NN - 1] = kr->mt[KR_MM - 1] ^ (x>>1) ^ mag01[(int)(x&1)];
- kr->mti = 0;
- }
- x = kr->mt[kr->mti++];
- x ^= (x >> 29) & 0x5555555555555555ULL;
- x ^= (x << 17) & 0x71D67FFFEDA60000ULL;
- x ^= (x << 37) & 0xFFF7EEE000000000ULL;
- x ^= (x >> 43);
- return x;
-}
-
-#ifdef _KR_MAIN
-int main(int argc, char *argv[])
-{
- long i, N = 200000000;
- krand_t *kr;
- if (argc > 1) N = atol(argv[1]);
- kr = kr_srand(11);
- for (i = 0; i < N; ++i) kr_rand(kr);
-// for (i = 0; i < N; ++i) lrand48();
- free(kr);
- return 0;
-}
-#endif
-
-/******************************
- *** Non-linear programming ***
- ******************************/
-
-/* Hooke-Jeeves algorithm for nonlinear minimization
-
- Based on the pseudocodes by Bell and Pike (CACM 9(9):684-685), and
- the revision by Tomlin and Smith (CACM 12(11):637-638). Both of the
- papers are comments on Kaupe's Algorithm 178 "Direct Search" (ACM
- 6(6):313-314). The original algorithm was designed by Hooke and
- Jeeves (ACM 8:212-229). This program is further revised according to
- Johnson's implementation at Netlib (opt/hooke.c).
-
- Hooke-Jeeves algorithm is very simple and it works quite well on a
- few examples. However, it might fail to converge due to its heuristic
- nature. A possible improvement, as is suggested by Johnson, may be to
- choose a small r at the beginning to quickly approach to the minimum
- and a large r at later step to hit the minimum.
- */
-
-static double __kmin_hj_aux(kmin_f func, int n, double *x1, void *data, double fx1, double *dx, int *n_calls)
-{
- int k, j = *n_calls;
- double ftmp;
- for (k = 0; k != n; ++k) {
- x1[k] += dx[k];
- ftmp = func(n, x1, data); ++j;
- if (ftmp < fx1) fx1 = ftmp;
- else { /* search the opposite direction */
- dx[k] = 0.0 - dx[k];
- x1[k] += dx[k] + dx[k];
- ftmp = func(n, x1, data); ++j;
- if (ftmp < fx1) fx1 = ftmp;
- else x1[k] -= dx[k]; /* back to the original x[k] */
- }
- }
- *n_calls = j;
- return fx1; /* here: fx1=f(n,x1) */
-}
-
-double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls)
-{
- double fx, fx1, *x1, *dx, radius;
- int k, n_calls = 0;
- x1 = (double*)calloc(n, sizeof(double));
- dx = (double*)calloc(n, sizeof(double));
- for (k = 0; k != n; ++k) { /* initial directions, based on MGJ */
- dx[k] = fabs(x[k]) * r;
- if (dx[k] == 0) dx[k] = r;
- }
- radius = r;
- fx1 = fx = func(n, x, data); ++n_calls;
- for (;;) {
- memcpy(x1, x, n * sizeof(double)); /* x1 = x */
- fx1 = __kmin_hj_aux(func, n, x1, data, fx, dx, &n_calls);
- while (fx1 < fx) {
- for (k = 0; k != n; ++k) {
- double t = x[k];
- dx[k] = x1[k] > x[k]? fabs(dx[k]) : 0.0 - fabs(dx[k]);
- x[k] = x1[k];
- x1[k] = x1[k] + x1[k] - t;
- }
- fx = fx1;
- if (n_calls >= max_calls) break;
- fx1 = func(n, x1, data); ++n_calls;
- fx1 = __kmin_hj_aux(func, n, x1, data, fx1, dx, &n_calls);
- if (fx1 >= fx) break;
- for (k = 0; k != n; ++k)
- if (fabs(x1[k] - x[k]) > .5 * fabs(dx[k])) break;
- if (k == n) break;
- }
- if (radius >= eps) {
- if (n_calls >= max_calls) break;
- radius *= r;
- for (k = 0; k != n; ++k) dx[k] *= r;
- } else break; /* converge */
- }
- free(x1); free(dx);
- return fx1;
-}
-
-// I copied this function somewhere several years ago with some of my modifications, but I forgot the source.
-double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin)
-{
- double bound, u, r, q, fu, tmp, fa, fb, fc, c;
- const double gold1 = 1.6180339887;
- const double gold2 = 0.3819660113;
- const double tiny = 1e-20;
- const int max_iter = 100;
-
- double e, d, w, v, mid, tol1, tol2, p, eold, fv, fw;
- int iter;
-
- fa = func(a, data); fb = func(b, data);
- if (fb > fa) { // swap, such that f(a) > f(b)
- tmp = a; a = b; b = tmp;
- tmp = fa; fa = fb; fb = tmp;
- }
- c = b + gold1 * (b - a), fc = func(c, data); // golden section extrapolation
- while (fb > fc) {
- bound = b + 100.0 * (c - b); // the farthest point where we want to go
- r = (b - a) * (fb - fc);
- q = (b - c) * (fb - fa);
- if (fabs(q - r) < tiny) { // avoid 0 denominator
- tmp = q > r? tiny : 0.0 - tiny;
- } else tmp = q - r;
- u = b - ((b - c) * q - (b - a) * r) / (2.0 * tmp); // u is the parabolic extrapolation point
- if ((b > u && u > c) || (b < u && u < c)) { // u lies between b and c
- fu = func(u, data);
- if (fu < fc) { // (b,u,c) bracket the minimum
- a = b; b = u; fa = fb; fb = fu;
- break;
- } else if (fu > fb) { // (a,b,u) bracket the minimum
- c = u; fc = fu;
- break;
- }
- u = c + gold1 * (c - b); fu = func(u, data); // golden section extrapolation
- } else if ((c > u && u > bound) || (c < u && u < bound)) { // u lies between c and bound
- fu = func(u, data);
- if (fu < fc) { // fb > fc > fu
- b = c; c = u; u = c + gold1 * (c - b);
- fb = fc; fc = fu; fu = func(u, data);
- } else { // (b,c,u) bracket the minimum
- a = b; b = c; c = u;
- fa = fb; fb = fc; fc = fu;
- break;
- }
- } else if ((u > bound && bound > c) || (u < bound && bound < c)) { // u goes beyond the bound
- u = bound; fu = func(u, data);
- } else { // u goes the other way around, use golden section extrapolation
- u = c + gold1 * (c - b); fu = func(u, data);
- }
- a = b; b = c; c = u;
- fa = fb; fb = fc; fc = fu;
- }
- if (a > c) u = a, a = c, c = u; // swap
-
- // now, a<b<c, fa>fb and fb<fc, move on to Brent's algorithm
- e = d = 0.0;
- w = v = b; fv = fw = fb;
- for (iter = 0; iter != max_iter; ++iter) {
- mid = 0.5 * (a + c);
- tol2 = 2.0 * (tol1 = tol * fabs(b) + tiny);
- if (fabs(b - mid) <= (tol2 - 0.5 * (c - a))) {
- *xmin = b; return fb; // found
- }
- if (fabs(e) > tol1) {
- // related to parabolic interpolation
- r = (b - w) * (fb - fv);
- q = (b - v) * (fb - fw);
- p = (b - v) * q - (b - w) * r;
- q = 2.0 * (q - r);
- if (q > 0.0) p = 0.0 - p;
- else q = 0.0 - q;
- eold = e; e = d;
- if (fabs(p) >= fabs(0.5 * q * eold) || p <= q * (a - b) || p >= q * (c - b)) {
- d = gold2 * (e = (b >= mid ? a - b : c - b));
- } else {
- d = p / q; u = b + d; // actual parabolic interpolation happens here
- if (u - a < tol2 || c - u < tol2)
- d = (mid > b)? tol1 : 0.0 - tol1;
- }
- } else d = gold2 * (e = (b >= mid ? a - b : c - b)); // golden section interpolation
- u = fabs(d) >= tol1 ? b + d : b + (d > 0.0? tol1 : -tol1);
- fu = func(u, data);
- if (fu <= fb) { // u is the minimum point so far
- if (u >= b) a = b;
- else c = b;
- v = w; w = b; b = u; fv = fw; fw = fb; fb = fu;
- } else { // adjust (a,c) and (u,v,w)
- if (u < b) a = u;
- else c = u;
- if (fu <= fw || w == b) {
- v = w; w = u;
- fv = fw; fw = fu;
- } else if (fu <= fv || v == b || v == w) {
- v = u; fv = fu;
- }
- }
- }
- *xmin = b;
- return fb;
-}
-
-/*************************
- *** Special functions ***
- *************************/
-
-/* Log gamma function
- * \log{\Gamma(z)}
- * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245
- */
-double kf_lgamma(double z)
-{
- double x = 0;
- x += 0.1659470187408462e-06 / (z+7);
- x += 0.9934937113930748e-05 / (z+6);
- x -= 0.1385710331296526 / (z+5);
- x += 12.50734324009056 / (z+4);
- x -= 176.6150291498386 / (z+3);
- x += 771.3234287757674 / (z+2);
- x -= 1259.139216722289 / (z+1);
- x += 676.5203681218835 / z;
- x += 0.9999999999995183;
- return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);
-}
-
-/* complementary error function
- * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt
- * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66
- */
-double kf_erfc(double x)
-{
- const double p0 = 220.2068679123761;
- const double p1 = 221.2135961699311;
- const double p2 = 112.0792914978709;
- const double p3 = 33.912866078383;
- const double p4 = 6.37396220353165;
- const double p5 = .7003830644436881;
- const double p6 = .03526249659989109;
- const double q0 = 440.4137358247522;
- const double q1 = 793.8265125199484;
- const double q2 = 637.3336333788311;
- const double q3 = 296.5642487796737;
- const double q4 = 86.78073220294608;
- const double q5 = 16.06417757920695;
- const double q6 = 1.755667163182642;
- const double q7 = .08838834764831844;
- double expntl, z, p;
- z = fabs(x) * M_SQRT2;
- if (z > 37.) return x > 0.? 0. : 2.;
- expntl = exp(z * z * - .5);
- if (z < 10. / M_SQRT2) // for small z
- p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0)
- / (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0);
- else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65)))));
- return x > 0.? 2. * p : 2. * (1. - p);
-}
-
-/* The following computes regularized incomplete gamma functions.
- * Formulas are taken from Wiki, with additional input from Numerical
- * Recipes in C (for modified Lentz's algorithm) and AS245
- * (http://lib.stat.cmu.edu/apstat/245).
- *
- * A good online calculator is available at:
- *
- * http://www.danielsoper.com/statcalc/calc23.aspx
- *
- * It calculates upper incomplete gamma function, which equals
- * kf_gammaq(s,z)*tgamma(s).
- */
-
-#define KF_GAMMA_EPS 1e-14
-#define KF_TINY 1e-290
-
-// regularized lower incomplete gamma function, by series expansion
-static double _kf_gammap(double s, double z)
-{
- double sum, x;
- int k;
- for (k = 1, sum = x = 1.; k < 100; ++k) {
- sum += (x *= z / (s + k));
- if (x / sum < KF_GAMMA_EPS) break;
- }
- return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum));
-}
-// regularized upper incomplete gamma function, by continued fraction
-static double _kf_gammaq(double s, double z)
-{
- int j;
- double C, D, f;
- f = 1. + z - s; C = f; D = 0.;
- // Modified Lentz's algorithm for computing continued fraction
- // See Numerical Recipes in C, 2nd edition, section 5.2
- for (j = 1; j < 100; ++j) {
- double a = j * (s - j), b = (j<<1) + 1 + z - s, d;
- D = b + a * D;
- if (D < KF_TINY) D = KF_TINY;
- C = b + a / C;
- if (C < KF_TINY) C = KF_TINY;
- D = 1. / D;
- d = C * D;
- f *= d;
- if (fabs(d - 1.) < KF_GAMMA_EPS) break;
- }
- return exp(s * log(z) - z - kf_lgamma(s) - log(f));
-}
-
-double kf_gammap(double s, double z)
-{
- return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z);
-}
-
-double kf_gammaq(double s, double z)
-{
- return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z);
-}
-
-/* Regularized incomplete beta function. The method is taken from
- * Numerical Recipe in C, 2nd edition, section 6.4. The following web
- * page calculates the incomplete beta function, which equals
- * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b):
- *
- * http://www.danielsoper.com/statcalc/calc36.aspx
- */
-static double kf_betai_aux(double a, double b, double x)
-{
- double C, D, f;
- int j;
- if (x == 0.) return 0.;
- if (x == 1.) return 1.;
- f = 1.; C = f; D = 0.;
- // Modified Lentz's algorithm for computing continued fraction
- for (j = 1; j < 200; ++j) {
- double aa, d;
- int m = j>>1;
- aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1))
- : m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m));
- D = 1. + aa * D;
- if (D < KF_TINY) D = KF_TINY;
- C = 1. + aa / C;
- if (C < KF_TINY) C = KF_TINY;
- D = 1. / D;
- d = C * D;
- f *= d;
- if (fabs(d - 1.) < KF_GAMMA_EPS) break;
- }
- return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f;
-}
-double kf_betai(double a, double b, double x)
-{
- return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x);
-}
-
-/******************
- *** Statistics ***
- ******************/
-
-double km_ks_dist(int na, const double a[], int nb, const double b[]) // a[] and b[] MUST BE sorted
-{
- int ia = 0, ib = 0;
- double fa = 0, fb = 0, sup = 0, na1 = 1. / na, nb1 = 1. / nb;
- while (ia < na || ib < nb) {
- if (ia == na) fb += nb1, ++ib;
- else if (ib == nb) fa += na1, ++ia;
- else if (a[ia] < b[ib]) fa += na1, ++ia;
- else if (a[ia] > b[ib]) fb += nb1, ++ib;
- else fa += na1, fb += nb1, ++ia, ++ib;
- if (sup < fabs(fa - fb)) sup = fabs(fa - fb);
- }
- return sup;
-}
-
-#ifdef KF_MAIN
-#include <stdio.h>
-#include "ksort.h"
-KSORT_INIT_GENERIC(double)
-int main(int argc, char *argv[])
-{
- double x = 5.5, y = 3;
- double a, b;
- double xx[] = {0.22, -0.87, -2.39, -1.79, 0.37, -1.54, 1.28, -0.31, -0.74, 1.72, 0.38, -0.17, -0.62, -1.10, 0.30, 0.15, 2.30, 0.19, -0.50, -0.09};
- double yy[] = {-5.13, -2.19, -2.43, -3.83, 0.50, -3.25, 4.32, 1.63, 5.18, -0.43, 7.11, 4.87, -3.10, -5.81, 3.76, 6.31, 2.58, 0.07, 5.76, 3.50};
- ks_introsort(double, 20, xx); ks_introsort(double, 20, yy);
- printf("K-S distance: %f\n", km_ks_dist(20, xx, 20, yy));
- printf("erfc(%lg): %lg, %lg\n", x, erfc(x), kf_erfc(x));
- printf("upper-gamma(%lg,%lg): %lg\n", x, y, kf_gammaq(y, x)*tgamma(y));
- a = 2; b = 2; x = 0.5;
- printf("incomplete-beta(%lg,%lg,%lg): %lg\n", a, b, x, kf_betai(a, b, x) / exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b)));
- return 0;
-}
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kmath.h b/debian/vendor-h2o/deps/klib/kmath.h
deleted file mode 100644
index 2c3e779..0000000
--- a/debian/vendor-h2o/deps/klib/kmath.h
+++ /dev/null
@@ -1,53 +0,0 @@
-#ifndef AC_KMATH_H
-#define AC_KMATH_H
-
-#include <stdint.h>
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- /**********************************
- * Pseudo-random number generator *
- **********************************/
-
- typedef uint64_t krint64_t;
-
- struct _krand_t;
- typedef struct _krand_t krand_t;
-
- #define kr_drand(_kr) ((kr_rand(_kr) >> 11) * (1.0/9007199254740992.0))
- #define kr_sample(_kr, _k, _cnt) ((*(_cnt))++ < (_k)? *(_cnt) - 1 : kr_rand(_kr) % *(_cnt))
-
- krand_t *kr_srand(krint64_t seed);
- krint64_t kr_rand(krand_t *kr);
-
- /**************************
- * Non-linear programming *
- **************************/
-
- #define KMIN_RADIUS 0.5
- #define KMIN_EPS 1e-7
- #define KMIN_MAXCALL 50000
-
- typedef double (*kmin_f)(int, double*, void*);
- typedef double (*kmin1_f)(double, void*);
-
- double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls); // Hooke-Jeeves'
- double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin); // Brent's 1-dimenssion
-
- /*********************
- * Special functions *
- *********************/
-
- double kf_lgamma(double z); // log gamma function
- double kf_erfc(double x); // complementary error function
- double kf_gammap(double s, double z); // regularized lower incomplete gamma function
- double kf_gammaq(double s, double z); // regularized upper incomplete gamma function
- double kf_betai(double a, double b, double x); // regularized incomplete beta function
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/knetfile.c b/debian/vendor-h2o/deps/klib/knetfile.c
deleted file mode 100644
index 158add9..0000000
--- a/debian/vendor-h2o/deps/klib/knetfile.c
+++ /dev/null
@@ -1,628 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 by Genome Research Ltd (GRL).
- 2010 by Attractive Chaos <attractor@live.co.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.
-*/
-
-/* Probably I will not do socket programming in the next few years and
- therefore I decide to heavily annotate this file, for Linux and
- Windows as well. -ac */
-
-#include <time.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <string.h>
-#include <errno.h>
-#include <unistd.h>
-#include <sys/types.h>
-
-#ifndef _WIN32
-#include <netdb.h>
-#include <arpa/inet.h>
-#include <sys/socket.h>
-#endif
-
-#include "knetfile.h"
-
-/* In winsock.h, the type of a socket is SOCKET, which is: "typedef
- * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed
- * integer -1. In knetfile.c, I use "int" for socket type
- * throughout. This should be improved to avoid confusion.
- *
- * In Linux/Mac, recv() and read() do almost the same thing. You can see
- * in the header file that netread() is simply an alias of read(). In
- * Windows, however, they are different and using recv() is mandatory.
- */
-
-/* This function tests if the file handler is ready for reading (or
- * writing if is_read==0). */
-static int socket_wait(int fd, int is_read)
-{
- fd_set fds, *fdr = 0, *fdw = 0;
- struct timeval tv;
- int ret;
- tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
- FD_ZERO(&fds);
- FD_SET(fd, &fds);
- if (is_read) fdr = &fds;
- else fdw = &fds;
- ret = select(fd+1, fdr, fdw, 0, &tv);
-#ifndef _WIN32
- if (ret == -1) perror("select");
-#else
- if (ret == 0)
- fprintf(stderr, "select time-out\n");
- else if (ret == SOCKET_ERROR)
- fprintf(stderr, "select: %d\n", WSAGetLastError());
-#endif
- return ret;
-}
-
-#ifndef _WIN32
-/* This function does not work with Windows due to the lack of
- * getaddrinfo() in winsock. It is addapted from an example in "Beej's
- * Guide to Network Programming" (http://beej.us/guide/bgnet/). */
-static int socket_connect(const char *host, const char *port)
-{
-#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
-
- int on = 1, fd;
- struct linger lng = { 0, 0 };
- struct addrinfo hints, *res = 0;
- memset(&hints, 0, sizeof(struct addrinfo));
- hints.ai_family = AF_UNSPEC;
- hints.ai_socktype = SOCK_STREAM;
- /* In Unix/Mac, getaddrinfo() is the most convenient way to get
- * server information. */
- if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
- if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
- /* The following two setsockopt() are used by ftplib
- * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they
- * necessary. */
- if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
- if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
- if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
- freeaddrinfo(res);
- return fd;
-}
-#else
-/* MinGW's printf has problem with "%lld" */
-char *int64tostr(char *buf, int64_t x)
-{
- int cnt;
- int i = 0;
- do {
- buf[i++] = '0' + x % 10;
- x /= 10;
- } while (x);
- buf[i] = 0;
- for (cnt = i, i = 0; i < cnt/2; ++i) {
- int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c;
- }
- return buf;
-}
-
-int64_t strtoint64(const char *buf)
-{
- int64_t x;
- for (x = 0; *buf != '\0'; ++buf)
- x = x * 10 + ((int64_t) *buf - 48);
- return x;
-}
-/* In windows, the first thing is to establish the TCP connection. */
-int knet_win32_init()
-{
- WSADATA wsaData;
- return WSAStartup(MAKEWORD(2, 2), &wsaData);
-}
-void knet_win32_destroy()
-{
- WSACleanup();
-}
-/* A slightly modfied version of the following function also works on
- * Mac (and presummably Linux). However, this function is not stable on
- * my Mac. It sometimes works fine but sometimes does not. Therefore for
- * non-Windows OS, I do not use this one. */
-static SOCKET socket_connect(const char *host, const char *port)
-{
-#define __err_connect(func) \
- do { \
- fprintf(stderr, "%s: %d\n", func, WSAGetLastError()); \
- return -1; \
- } while (0)
-
- int on = 1;
- SOCKET fd;
- struct linger lng = { 0, 0 };
- struct sockaddr_in server;
- struct hostent *hp = 0;
- // open socket
- if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket");
- if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt");
- if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt");
- // get host info
- if (isalpha(host[0])) hp = gethostbyname(host);
- else {
- struct in_addr addr;
- addr.s_addr = inet_addr(host);
- hp = gethostbyaddr((char*)&addr, 4, AF_INET);
- }
- if (hp == 0) __err_connect("gethost");
- // connect
- server.sin_addr.s_addr = *((unsigned long*)hp->h_addr);
- server.sin_family= AF_INET;
- server.sin_port = htons(atoi(port));
- if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect");
- // freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!)
- return fd;
-}
-#endif
-
-static off_t my_netread(int fd, void *buf, off_t len)
-{
- off_t rest = len, curr, l = 0;
- /* recv() and read() may not read the required length of data with
- * one call. They have to be called repeatedly. */
- while (rest) {
- if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading
- curr = netread(fd, buf + l, rest);
- /* According to the glibc manual, section 13.2, a zero returned
- * value indicates end-of-file (EOF), which should mean that
- * read() will not return zero if EOF has not been met but data
- * are not immediately available. */
- if (curr == 0) break;
- l += curr; rest -= curr;
- }
- return l;
-}
-
-/*************************
- * FTP specific routines *
- *************************/
-
-static int kftp_get_response(knetFile *ftp)
-{
-#ifndef _WIN32
- unsigned char c;
-#else
- char c;
-#endif
- int n = 0;
- char *p;
- if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0;
- while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
- //fputc(c, stderr);
- if (n >= ftp->max_response) {
- ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256;
- ftp->response = (char*)realloc(ftp->response, ftp->max_response);
- }
- ftp->response[n++] = c;
- if (c == '\n') {
- if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2])
- && ftp->response[3] != '-') break;
- n = 0;
- continue;
- }
- }
- if (n < 2) return -1;
- ftp->response[n-2] = 0;
- return strtol(ftp->response, &p, 0);
-}
-
-static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get)
-{
- if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
- netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
- return is_get? kftp_get_response(ftp) : 0;
-}
-
-static int kftp_pasv_prep(knetFile *ftp)
-{
- char *p;
- int v[6];
- kftp_send_cmd(ftp, "PASV\r\n", 1);
- for (p = ftp->response; *p && *p != '('; ++p);
- if (*p != '(') return -1;
- ++p;
- sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
- memcpy(ftp->pasv_ip, v, 4 * sizeof(int));
- ftp->pasv_port = (v[4]<<8&0xff00) + v[5];
- return 0;
-}
-
-
-static int kftp_pasv_connect(knetFile *ftp)
-{
- char host[80], port[10];
- if (ftp->pasv_port == 0) {
- fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n");
- return -1;
- }
- sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]);
- sprintf(port, "%d", ftp->pasv_port);
- ftp->fd = socket_connect(host, port);
- if (ftp->fd == -1) return -1;
- return 0;
-}
-
-int kftp_connect(knetFile *ftp)
-{
- ftp->ctrl_fd = socket_connect(ftp->host, ftp->port);
- if (ftp->ctrl_fd == -1) return -1;
- kftp_get_response(ftp);
- kftp_send_cmd(ftp, "USER anonymous\r\n", 1);
- kftp_send_cmd(ftp, "PASS kftp@\r\n", 1);
- kftp_send_cmd(ftp, "TYPE I\r\n", 1);
- return 0;
-}
-
-int kftp_reconnect(knetFile *ftp)
-{
- if (ftp->ctrl_fd != -1) {
- netclose(ftp->ctrl_fd);
- ftp->ctrl_fd = -1;
- }
- netclose(ftp->fd);
- ftp->fd = -1;
- return kftp_connect(ftp);
-}
-
-// initialize ->type, ->host, ->retr and ->size
-knetFile *kftp_parse_url(const char *fn, const char *mode)
-{
- knetFile *fp;
- char *p;
- int l;
- if (strstr(fn, "ftp://") != fn) return 0;
- for (p = (char*)fn + 6; *p && *p != '/'; ++p);
- if (*p != '/') return 0;
- l = p - fn - 6;
- fp = (knetFile*)calloc(1, sizeof(knetFile));
- fp->type = KNF_TYPE_FTP;
- fp->fd = -1;
- /* the Linux/Mac version of socket_connect() also recognizes a port
- * like "ftp", but the Windows version does not. */
- fp->port = strdup("21");
- fp->host = (char*)calloc(l + 1, 1);
- if (strchr(mode, 'c')) fp->no_reconnect = 1;
- strncpy(fp->host, fn + 6, l);
- fp->retr = (char*)calloc(strlen(p) + 8, 1);
- sprintf(fp->retr, "RETR %s\r\n", p);
- fp->size_cmd = (char*)calloc(strlen(p) + 8, 1);
- sprintf(fp->size_cmd, "SIZE %s\r\n", p);
- fp->seek_offset = 0;
- return fp;
-}
-// place ->fd at offset off
-int kftp_connect_file(knetFile *fp)
-{
- int ret;
- long long file_size;
- if (fp->fd != -1) {
- netclose(fp->fd);
- if (fp->no_reconnect) kftp_get_response(fp);
- }
- kftp_pasv_prep(fp);
- kftp_send_cmd(fp, fp->size_cmd, 1);
-#ifndef _WIN32
- if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 )
- {
- fprintf(stderr,"[kftp_connect_file] %s\n", fp->response);
- return -1;
- }
-#else
- const char *p = fp->response;
- while (*p != ' ') ++p;
- while (*p < '0' || *p > '9') ++p;
- file_size = strtoint64(p);
-#endif
- fp->file_size = file_size;
- if (fp->offset>=0) {
- char tmp[32];
-#ifndef _WIN32
- sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
-#else
- strcpy(tmp, "REST ");
- int64tostr(tmp + 5, fp->offset);
- strcat(tmp, "\r\n");
-#endif
- kftp_send_cmd(fp, tmp, 1);
- }
- kftp_send_cmd(fp, fp->retr, 0);
- kftp_pasv_connect(fp);
- ret = kftp_get_response(fp);
- if (ret != 150) {
- fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
- netclose(fp->fd);
- fp->fd = -1;
- return -1;
- }
- fp->is_ready = 1;
- return 0;
-}
-
-
-/**************************
- * HTTP specific routines *
- **************************/
-
-knetFile *khttp_parse_url(const char *fn, const char *mode)
-{
- knetFile *fp;
- char *p, *proxy, *q;
- int l;
- if (strstr(fn, "http://") != fn) return 0;
- // set ->http_host
- for (p = (char*)fn + 7; *p && *p != '/'; ++p);
- l = p - fn - 7;
- fp = (knetFile*)calloc(1, sizeof(knetFile));
- fp->http_host = (char*)calloc(l + 1, 1);
- strncpy(fp->http_host, fn + 7, l);
- fp->http_host[l] = 0;
- for (q = fp->http_host; *q && *q != ':'; ++q);
- if (*q == ':') *q++ = 0;
- // get http_proxy
- proxy = getenv("http_proxy");
- // set ->host, ->port and ->path
- if (proxy == 0) {
- fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name.
- fp->port = strdup(*q? q : "80");
- fp->path = strdup(*p? p : "/");
- } else {
- fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
- for (q = fp->host; *q && *q != ':'; ++q);
- if (*q == ':') *q++ = 0;
- fp->port = strdup(*q? q : "80");
- fp->path = strdup(fn);
- }
- fp->type = KNF_TYPE_HTTP;
- fp->ctrl_fd = fp->fd = -1;
- fp->seek_offset = 0;
- return fp;
-}
-
-int khttp_connect_file(knetFile *fp)
-{
- int ret, l = 0;
- char *buf, *p;
- if (fp->fd != -1) netclose(fp->fd);
- fp->fd = socket_connect(fp->host, fp->port);
- buf = (char*)calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
- l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host);
- l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
- l += sprintf(buf + l, "\r\n");
- netwrite(fp->fd, buf, l);
- l = 0;
- while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
- if (buf[l] == '\n' && l >= 3)
- if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
- ++l;
- }
- buf[l] = 0;
- if (l < 14) { // prematured header
- netclose(fp->fd);
- fp->fd = -1;
- return -1;
- }
- ret = strtol(buf + 8, &p, 0); // HTTP return code
- if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file
- off_t rest = fp->offset;
- while (rest) {
- off_t l = rest < 0x10000? rest : 0x10000;
- rest -= my_netread(fp->fd, buf, l);
- }
- } else if (ret != 206 && ret != 200) {
- free(buf);
- fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret);
- netclose(fp->fd);
- fp->fd = -1;
- return -1;
- }
- free(buf);
- fp->is_ready = 1;
- return 0;
-}
-
-/********************
- * Generic routines *
- ********************/
-
-knetFile *knet_open(const char *fn, const char *mode)
-{
- knetFile *fp = 0;
- if (mode[0] != 'r') {
- fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n");
- return 0;
- }
- if (strstr(fn, "ftp://") == fn) {
- fp = kftp_parse_url(fn, mode);
- if (fp == 0) return 0;
- if (kftp_connect(fp) == -1) {
- knet_close(fp);
- return 0;
- }
- kftp_connect_file(fp);
- } else if (strstr(fn, "http://") == fn) {
- fp = khttp_parse_url(fn, mode);
- if (fp == 0) return 0;
- khttp_connect_file(fp);
- } else { // local file
-#ifdef _WIN32
- /* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may
- * be undefined on some systems, although it is defined on my
- * Mac and the Linux I have tested on. */
- int fd = open(fn, O_RDONLY | O_BINARY);
-#else
- int fd = open(fn, O_RDONLY);
-#endif
- if (fd == -1) {
- perror("open");
- return 0;
- }
- fp = (knetFile*)calloc(1, sizeof(knetFile));
- fp->type = KNF_TYPE_LOCAL;
- fp->fd = fd;
- fp->ctrl_fd = -1;
- }
- if (fp && fp->fd == -1) {
- knet_close(fp);
- return 0;
- }
- return fp;
-}
-
-knetFile *knet_dopen(int fd, const char *mode)
-{
- knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile));
- fp->type = KNF_TYPE_LOCAL;
- fp->fd = fd;
- return fp;
-}
-
-off_t knet_read(knetFile *fp, void *buf, off_t len)
-{
- off_t l = 0;
- if (fp->fd == -1) return 0;
- if (fp->type == KNF_TYPE_FTP) {
- if (fp->is_ready == 0) {
- if (!fp->no_reconnect) kftp_reconnect(fp);
- kftp_connect_file(fp);
- }
- } else if (fp->type == KNF_TYPE_HTTP) {
- if (fp->is_ready == 0)
- khttp_connect_file(fp);
- }
- if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX
- off_t rest = len, curr;
- while (rest) {
- do {
- curr = read(fp->fd, buf + l, rest);
- } while (curr < 0 && EINTR == errno);
- if (curr < 0) return -1;
- if (curr == 0) break;
- l += curr; rest -= curr;
- }
- } else l = my_netread(fp->fd, buf, len);
- fp->offset += l;
- return l;
-}
-
-off_t knet_seek(knetFile *fp, int64_t off, int whence)
-{
- if (whence == SEEK_SET && off == fp->offset) return 0;
- if (fp->type == KNF_TYPE_LOCAL) {
- /* Be aware that lseek() returns the offset after seeking,
- * while fseek() returns zero on success. */
- off_t offset = lseek(fp->fd, off, whence);
- if (offset == -1) {
- // Be silent, it is OK for knet_seek to fail when the file is streamed
- // fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
- return -1;
- }
- fp->offset = offset;
- return off;
- } else if (fp->type == KNF_TYPE_FTP) {
- if (whence==SEEK_CUR)
- fp->offset += off;
- else if (whence==SEEK_SET)
- fp->offset = off;
- else if ( whence==SEEK_END)
- fp->offset = fp->file_size+off;
- fp->is_ready = 0;
- return off;
- } else if (fp->type == KNF_TYPE_HTTP) {
- if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future?
- fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n");
- errno = ESPIPE;
- return -1;
- }
- if (whence==SEEK_CUR)
- fp->offset += off;
- else if (whence==SEEK_SET)
- fp->offset = off;
- fp->is_ready = 0;
- return off;
- }
- errno = EINVAL;
- fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
- return -1;
-}
-
-int knet_close(knetFile *fp)
-{
- if (fp == 0) return 0;
- if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific
- if (fp->fd != -1) {
- /* On Linux/Mac, netclose() is an alias of close(), but on
- * Windows, it is an alias of closesocket(). */
- if (fp->type == KNF_TYPE_LOCAL) close(fp->fd);
- else netclose(fp->fd);
- }
- free(fp->host); free(fp->port);
- free(fp->response); free(fp->retr); // FTP specific
- free(fp->path); free(fp->http_host); // HTTP specific
- free(fp);
- return 0;
-}
-
-#ifdef KNETFILE_MAIN
-int main(void)
-{
- char *buf;
- knetFile *fp;
- int type = 4, l;
-#ifdef _WIN32
- knet_win32_init();
-#endif
- buf = calloc(0x100000, 1);
- if (type == 0) {
- fp = knet_open("knetfile.c", "r");
- knet_seek(fp, 1000, SEEK_SET);
- } else if (type == 1) { // NCBI FTP, large file
- fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r");
- knet_seek(fp, 2500000000ll, SEEK_SET);
- l = knet_read(fp, buf, 255);
- } else if (type == 2) {
- fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r");
- knet_seek(fp, 1000, SEEK_SET);
- } else if (type == 3) {
- fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r");
- knet_seek(fp, 1000, SEEK_SET);
- } else if (type == 4) {
- fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
- knet_read(fp, buf, 10000);
- knet_seek(fp, 20000, SEEK_SET);
- knet_seek(fp, 10000, SEEK_SET);
- l = knet_read(fp, buf+10000, 10000000) + 10000;
- }
- if (type != 4 && type != 1) {
- knet_read(fp, buf, 255);
- buf[255] = 0;
- printf("%s\n", buf);
- } else write(fileno(stdout), buf, l);
- knet_close(fp);
- free(buf);
- return 0;
-}
-#endif
diff --git a/debian/vendor-h2o/deps/klib/knetfile.h b/debian/vendor-h2o/deps/klib/knetfile.h
deleted file mode 100644
index 0a0e66f..0000000
--- a/debian/vendor-h2o/deps/klib/knetfile.h
+++ /dev/null
@@ -1,75 +0,0 @@
-#ifndef KNETFILE_H
-#define KNETFILE_H
-
-#include <stdint.h>
-#include <fcntl.h>
-
-#ifndef _WIN32
-#define netread(fd, ptr, len) read(fd, ptr, len)
-#define netwrite(fd, ptr, len) write(fd, ptr, len)
-#define netclose(fd) close(fd)
-#else
-#include <winsock2.h>
-#define netread(fd, ptr, len) recv(fd, ptr, len, 0)
-#define netwrite(fd, ptr, len) send(fd, ptr, len, 0)
-#define netclose(fd) closesocket(fd)
-#endif
-
-// FIXME: currently I/O is unbuffered
-
-#define KNF_TYPE_LOCAL 1
-#define KNF_TYPE_FTP 2
-#define KNF_TYPE_HTTP 3
-
-typedef struct knetFile_s {
- int type, fd;
- int64_t offset;
- char *host, *port;
-
- // the following are for FTP only
- int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready;
- char *response, *retr, *size_cmd;
- int64_t seek_offset; // for lazy seek
- int64_t file_size;
-
- // the following are for HTTP only
- char *path, *http_host;
-} knetFile;
-
-#define knet_tell(fp) ((fp)->offset)
-#define knet_fileno(fp) ((fp)->fd)
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#ifdef _WIN32
- int knet_win32_init();
- void knet_win32_destroy();
-#endif
-
- knetFile *knet_open(const char *fn, const char *mode);
-
- /*
- This only works with local files.
- */
- knetFile *knet_dopen(int fd, const char *mode);
-
- /*
- If ->is_ready==0, this routine updates ->fd; otherwise, it simply
- reads from ->fd.
- */
- off_t knet_read(knetFile *fp, void *buf, off_t len);
-
- /*
- This routine only sets ->offset and ->is_ready=0. It does not
- communicate with the FTP server.
- */
- off_t knet_seek(knetFile *fp, int64_t off, int whence);
- int knet_close(knetFile *fp);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/knhx.c b/debian/vendor-h2o/deps/klib/knhx.c
deleted file mode 100644
index 8dbd3b6..0000000
--- a/debian/vendor-h2o/deps/klib/knhx.c
+++ /dev/null
@@ -1,166 +0,0 @@
-#include <ctype.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include "knhx.h"
-
-typedef struct {
- int error, n, max;
- knhx1_t *node;
-} knaux_t;
-
-static inline char *add_node(const char *s, knaux_t *aux, int x)
-{
- char *p, *nbeg, *nend = 0;
- knhx1_t *r;
- if (aux->n == aux->max) {
- aux->max = aux->max? aux->max<<1 : 8;
- aux->node = (knhx1_t*)realloc(aux->node, sizeof(knhx1_t) * aux->max);
- }
- r = aux->node + (aux->n++);
- r->n = x; r->parent = -1;
- for (p = (char*)s, nbeg = p, r->d = -1.0; *p && *p != ',' && *p != ')'; ++p) {
- if (*p == '[') {
- if (nend == 0) nend = p;
- do ++p; while (*p && *p != ']');
- if (*p == 0) {
- aux->error |= KNERR_BRACKET;
- break;
- }
- } else if (*p == ':') {
- if (nend == 0) nend = p;
- r->d = strtod(p + 1, &p);
- --p;
- } else if (!isgraph(*p)) if (nend == 0) nend = p;
- }
- if (nend == 0) nend = p;
- if (nend != nbeg) {
- r->name = (char*)calloc(nend - nbeg + 1, 1);
- strncpy(r->name, nbeg, nend - nbeg);
- } else r->name = strdup("");
- return p;
-}
-
-knhx1_t *kn_parse(const char *nhx, int *_n, int *_error)
-{
- char *p;
- int *stack, top, max;
- knaux_t *aux;
- knhx1_t *ret;
-
-#define __push_back(y) do { \
- if (top == max) { \
- max = max? max<<1 : 16; \
- stack = (int*)realloc(stack, sizeof(int) * max); \
- } \
- stack[top++] = (y); \
- } while (0) \
-
- stack = 0; top = max = 0;
- p = (char*)nhx;
- aux = (knaux_t*)calloc(1, sizeof(knaux_t));
- while (*p) {
- while (*p && !isgraph(*p)) ++p;
- if (*p == 0) break;
- if (*p == ',') ++p;
- else if (*p == '(') {
- __push_back(-1);
- ++p;
- } else if (*p == ')') {
- int x = aux->n, m, i;
- for (i = top - 1; i >= 0; --i)
- if (stack[i] < 0) break;
- m = top - 1 - i;
- p = add_node(p + 1, aux, m);
- aux->node[x].child = (int*)calloc(m, sizeof(int));
- for (i = top - 1, m = m - 1; m >= 0; --m, --i) {
- aux->node[x].child[m] = stack[i];
- aux->node[stack[i]].parent = x;
- }
- top = i;
- __push_back(x);
- } else {
- __push_back(aux->n);
- p = add_node(p, aux, 0);
- }
- }
- *_n = aux->n;
- *_error = aux->error;
- ret = aux->node;
- free(aux); free(stack);
- return ret;
-}
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-static inline int kputsn(const char *p, int l, kstring_t *s)
-{
- if (s->l + l + 1 >= s->m) {
- s->m = s->l + l + 2;
- kroundup32(s->m);
- s->s = (char*)realloc(s->s, s->m);
- }
- memcpy(s->s + s->l, p, l);
- s->l += l; s->s[s->l] = 0;
- return l;
-}
-
-static inline int kputc(int c, kstring_t *s)
-{
- if (s->l + 1 >= s->m) {
- s->m = s->l + 2;
- kroundup32(s->m);
- s->s = (char*)realloc(s->s, s->m);
- }
- s->s[s->l++] = c; s->s[s->l] = 0;
- return c;
-}
-
-static void format_node_recur(const knhx1_t *node, const knhx1_t *p, kstring_t *s, char *numbuf)
-{
- if (p->n) {
- int i;
- kputc('(', s);
- for (i = 0; i < p->n; ++i) {
- if (i) kputc(',', s);
- format_node_recur(node, &node[p->child[i]], s, numbuf);
- }
- kputc(')', s);
- if (p->name) kputsn(p->name, strlen(p->name), s);
- if (p->d >= 0) {
- sprintf(numbuf, ":%g", p->d);
- kputsn(numbuf, strlen(numbuf), s);
- }
- } else kputsn(p->name, strlen(p->name), s);
-}
-
-void kn_format(const knhx1_t *node, int root, kstring_t *s) // TODO: get rid of recursion
-{
- char numbuf[128];
- format_node_recur(node, &node[root], s, numbuf);
-}
-
-#ifdef KNHX_MAIN
-int main(int argc, char *argv[])
-{
- char *s = "((a[abc],d1)x:0.5,((b[&&NHX:S=MOUSE],h2)[&&NHX:S=HUMAN:B=99][blabla][&&NHX:K=foo],c))";
- knhx1_t *node;
- int i, j, n, error;
- kstring_t str;
- node = kn_parse(s, &n, &error);
- for (i = 0; i < n; ++i) {
- knhx1_t *p = node + i;
- printf("[%d] %s\t%d\t%d\t%g", i, p->name, p->parent, p->n, p->d);
- for (j = 0; j < p->n; ++j)
- printf("\t%d", p->child[j]);
- putchar('\n');
- }
- str.l = str.m = 0; str.s = 0;
- kn_format(node, n-1, &str);
- puts(str.s);
- free(str.s);
- return 0;
-}
-#endif
diff --git a/debian/vendor-h2o/deps/klib/knhx.h b/debian/vendor-h2o/deps/klib/knhx.h
deleted file mode 100644
index dbad7dd..0000000
--- a/debian/vendor-h2o/deps/klib/knhx.h
+++ /dev/null
@@ -1,35 +0,0 @@
-#ifndef KNHX_H_
-#define KNHX_H_
-
-#define KNERR_MISSING_LEFT 0x01
-#define KNERR_MISSING_RGHT 0x02
-#define KNERR_BRACKET 0x04
-#define KNERR_COLON 0x08
-
-typedef struct {
- int parent, n;
- int *child;
- char *name;
- double d;
-} knhx1_t;
-
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct __kstring_t {
- size_t l, m;
- char *s;
-} kstring_t;
-#endif
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- knhx1_t *kn_parse(const char *nhx, int *_n, int *_error);
- void kn_format(const knhx1_t *node, int root, kstring_t *s);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kopen.c b/debian/vendor-h2o/deps/klib/kopen.c
deleted file mode 100644
index f72735c..0000000
--- a/debian/vendor-h2o/deps/klib/kopen.c
+++ /dev/null
@@ -1,343 +0,0 @@
-#include <stdio.h>
-#include <fcntl.h>
-#include <errno.h>
-#include <ctype.h>
-#include <unistd.h>
-#include <string.h>
-#include <stdlib.h>
-#include <signal.h>
-#include <sys/types.h>
-#ifndef _WIN32
-#include <netdb.h>
-#include <arpa/inet.h>
-#include <sys/socket.h>
-#endif
-
-#ifdef _WIN32
-#define _KO_NO_NET
-#endif
-
-#ifndef _KO_NO_NET
-static int socket_wait(int fd, int is_read)
-{
- fd_set fds, *fdr = 0, *fdw = 0;
- struct timeval tv;
- int ret;
- tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
- FD_ZERO(&fds);
- FD_SET(fd, &fds);
- if (is_read) fdr = &fds;
- else fdw = &fds;
- ret = select(fd+1, fdr, fdw, 0, &tv);
- if (ret == -1) perror("select");
- return ret;
-}
-
-static int socket_connect(const char *host, const char *port)
-{
-#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
-
- int on = 1, fd;
- struct linger lng = { 0, 0 };
- struct addrinfo hints, *res = 0;
- memset(&hints, 0, sizeof(struct addrinfo));
- hints.ai_family = AF_UNSPEC;
- hints.ai_socktype = SOCK_STREAM;
- if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
- if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
- if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
- if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
- if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
- freeaddrinfo(res);
- return fd;
-#undef __err_connect
-}
-
-static int http_open(const char *fn)
-{
- char *p, *proxy, *q, *http_host, *host, *port, *path, *buf;
- int fd, ret, l;
-
- /* parse URL; adapted from khttp_parse_url() in knetfile.c */
- if (strstr(fn, "http://") != fn) return 0;
- // set ->http_host
- for (p = (char*)fn + 7; *p && *p != '/'; ++p);
- l = p - fn - 7;
- http_host = calloc(l + 1, 1);
- strncpy(http_host, fn + 7, l);
- http_host[l] = 0;
- for (q = http_host; *q && *q != ':'; ++q);
- if (*q == ':') *q++ = 0;
- // get http_proxy
- proxy = getenv("http_proxy");
- // set host, port and path
- if (proxy == 0) {
- host = strdup(http_host); // when there is no proxy, server name is identical to http_host name.
- port = strdup(*q? q : "80");
- path = strdup(*p? p : "/");
- } else {
- host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
- for (q = host; *q && *q != ':'; ++q);
- if (*q == ':') *q++ = 0;
- port = strdup(*q? q : "80");
- path = strdup(fn);
- }
-
- /* connect; adapted from khttp_connect() in knetfile.c */
- l = 0;
- fd = socket_connect(host, port);
- buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
- l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", path, http_host);
- l += sprintf(buf + l, "\r\n");
- write(fd, buf, l);
- l = 0;
- while (read(fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
- if (buf[l] == '\n' && l >= 3)
- if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
- ++l;
- }
- buf[l] = 0;
- if (l < 14) { // prematured header
- close(fd);
- fd = -1;
- }
- ret = strtol(buf + 8, &p, 0); // HTTP return code
- if (ret != 200) {
- close(fd);
- fd = -1;
- }
- free(buf); free(http_host); free(host); free(port); free(path);
- return fd;
-}
-
-typedef struct {
- int max_response, ctrl_fd;
- char *response;
-} ftpaux_t;
-
-static int kftp_get_response(ftpaux_t *aux)
-{
- unsigned char c;
- int n = 0;
- char *p;
- if (socket_wait(aux->ctrl_fd, 1) <= 0) return 0;
- while (read(aux->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
- if (n >= aux->max_response) {
- aux->max_response = aux->max_response? aux->max_response<<1 : 256;
- aux->response = realloc(aux->response, aux->max_response);
- }
- aux->response[n++] = c;
- if (c == '\n') {
- if (n >= 4 && isdigit(aux->response[0]) && isdigit(aux->response[1]) && isdigit(aux->response[2])
- && aux->response[3] != '-') break;
- n = 0;
- continue;
- }
- }
- if (n < 2) return -1;
- aux->response[n-2] = 0;
- return strtol(aux->response, &p, 0);
-}
-
-static int kftp_send_cmd(ftpaux_t *aux, const char *cmd, int is_get)
-{
- if (socket_wait(aux->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
- write(aux->ctrl_fd, cmd, strlen(cmd));
- return is_get? kftp_get_response(aux) : 0;
-}
-
-static int ftp_open(const char *fn)
-{
- char *p, *host = 0, *port = 0, *retr = 0;
- char host2[80], port2[10];
- int v[6], l, fd = -1, ret, pasv_port, pasv_ip[4];
- ftpaux_t aux;
-
- /* parse URL */
- if (strstr(fn, "ftp://") != fn) return 0;
- for (p = (char*)fn + 6; *p && *p != '/'; ++p);
- if (*p != '/') return 0;
- l = p - fn - 6;
- port = strdup("21");
- host = calloc(l + 1, 1);
- strncpy(host, fn + 6, l);
- retr = calloc(strlen(p) + 8, 1);
- sprintf(retr, "RETR %s\r\n", p);
-
- /* connect to ctrl */
- memset(&aux, 0, sizeof(ftpaux_t));
- aux.ctrl_fd = socket_connect(host, port);
- if (aux.ctrl_fd == -1) goto ftp_open_end; /* fail to connect ctrl */
-
- /* connect to the data stream */
- kftp_get_response(&aux);
- kftp_send_cmd(&aux, "USER anonymous\r\n", 1);
- kftp_send_cmd(&aux, "PASS kopen@\r\n", 1);
- kftp_send_cmd(&aux, "TYPE I\r\n", 1);
- kftp_send_cmd(&aux, "PASV\r\n", 1);
- for (p = aux.response; *p && *p != '('; ++p);
- if (*p != '(') goto ftp_open_end;
- ++p;
- sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
- memcpy(pasv_ip, v, 4 * sizeof(int));
- pasv_port = (v[4]<<8&0xff00) + v[5];
- kftp_send_cmd(&aux, retr, 0);
- sprintf(host2, "%d.%d.%d.%d", pasv_ip[0], pasv_ip[1], pasv_ip[2], pasv_ip[3]);
- sprintf(port2, "%d", pasv_port);
- fd = socket_connect(host2, port2);
- if (fd == -1) goto ftp_open_end;
- ret = kftp_get_response(&aux);
- if (ret != 150) {
- close(fd);
- fd = -1;
- }
- close(aux.ctrl_fd);
-
-ftp_open_end:
- free(host); free(port); free(retr); free(aux.response);
- return fd;
-}
-#endif /* !defined(_KO_NO_NET) */
-
-static char **cmd2argv(const char *cmd)
-{
- int i, beg, end, argc;
- char **argv, *p, *q, *str;
- end = strlen(cmd);
- for (i = end - 1; i >= 0; --i)
- if (!isspace(cmd[i])) break;
- end = i + 1;
- for (beg = 0; beg < end; ++beg)
- if (!isspace(cmd[beg])) break;
- if (beg == end) return 0;
- for (i = beg + 1, argc = 0; i < end; ++i)
- if (isspace(cmd[i]) && !isspace(cmd[i-1]))
- ++argc;
- argv = (char**)calloc(argc + 2, sizeof(void*));
- argv[0] = str = (char*)calloc(end - beg + 1, 1);
- strncpy(argv[0], cmd + beg, end - beg);
- for (i = argc = 1, q = p = str; i < end - beg; ++i)
- if (isspace(str[i])) str[i] = 0;
- else if (str[i] && str[i-1] == 0) argv[argc++] = &str[i];
- return argv;
-}
-
-#define KO_STDIN 1
-#define KO_FILE 2
-#define KO_PIPE 3
-#define KO_HTTP 4
-#define KO_FTP 5
-
-typedef struct {
- int type, fd;
- pid_t pid;
-} koaux_t;
-
-void *kopen(const char *fn, int *_fd)
-{
- koaux_t *aux = 0;
- *_fd = -1;
- if (strstr(fn, "http://") == fn) {
- aux = calloc(1, sizeof(koaux_t));
- aux->type = KO_HTTP;
- aux->fd = http_open(fn);
- } else if (strstr(fn, "ftp://") == fn) {
- aux = calloc(1, sizeof(koaux_t));
- aux->type = KO_FTP;
- aux->fd = ftp_open(fn);
- } else if (strcmp(fn, "-") == 0) {
- aux = calloc(1, sizeof(koaux_t));
- aux->type = KO_STDIN;
- aux->fd = STDIN_FILENO;
- } else {
- const char *p, *q;
- for (p = fn; *p; ++p)
- if (!isspace(*p)) break;
- if (*p == '<') { // pipe open
- int need_shell, pfd[2];
- pid_t pid;
- // a simple check to see if we need to invoke a shell; not always working
- for (q = p + 1; *q; ++q)
- if (ispunct(*q) && *q != '.' && *q != '_' && *q != '-' && *q != ':')
- break;
- need_shell = (*q != 0);
- pipe(pfd);
- pid = vfork();
- if (pid == -1) { /* vfork() error */
- close(pfd[0]); close(pfd[1]);
- return 0;
- }
- if (pid == 0) { /* the child process */
- char **argv; /* FIXME: I do not know if this will lead to a memory leak */
- close(pfd[0]);
- dup2(pfd[1], STDOUT_FILENO);
- close(pfd[1]);
- if (!need_shell) {
- argv = cmd2argv(p + 1);
- execvp(argv[0], argv);
- free(argv[0]); free(argv);
- } else execl("/bin/sh", "sh", "-c", p + 1, NULL);
- exit(1);
- } else { /* parent process */
- close(pfd[1]);
- aux = calloc(1, sizeof(koaux_t));
- aux->type = KO_PIPE;
- aux->fd = pfd[0];
- aux->pid = pid;
- }
- } else {
-#ifdef _WIN32
- *_fd = open(fn, O_RDONLY | O_BINARY);
-#else
- *_fd = open(fn, O_RDONLY);
-#endif
- if (*_fd) {
- aux = calloc(1, sizeof(koaux_t));
- aux->type = KO_FILE;
- aux->fd = *_fd;
- }
- }
- }
- *_fd = aux->fd;
- return aux;
-}
-
-int kclose(void *a)
-{
- koaux_t *aux = (koaux_t*)a;
- if (aux->type == KO_PIPE) {
- int status;
- pid_t pid;
- pid = waitpid(aux->pid, &status, WNOHANG);
- if (pid != aux->pid) kill(aux->pid, 15);
- }
- return 0;
-}
-
-#ifdef _KO_MAIN
-#define BUF_SIZE 0x10000
-int main(int argc, char *argv[])
-{
- void *x;
- int l, fd;
- unsigned char buf[BUF_SIZE];
- FILE *fp;
- if (argc == 1) {
- fprintf(stderr, "Usage: kopen <file>\n");
- return 1;
- }
- x = kopen(argv[1], &fd);
- fp = fdopen(fd, "r");
- if (fp == 0) {
- fprintf(stderr, "ERROR: fail to open the input\n");
- return 1;
- }
- do {
- if ((l = fread(buf, 1, BUF_SIZE, fp)) != 0)
- fwrite(buf, 1, l, stdout);
- } while (l == BUF_SIZE);
- fclose(fp);
- kclose(x);
- return 0;
-}
-#endif
diff --git a/debian/vendor-h2o/deps/klib/ksa.c b/debian/vendor-h2o/deps/klib/ksa.c
deleted file mode 100644
index 18f686d..0000000
--- a/debian/vendor-h2o/deps/klib/ksa.c
+++ /dev/null
@@ -1,242 +0,0 @@
-/*
- * Copyright (c) 2008 Yuta Mori All Rights Reserved.
- * 2011 Attractive Chaos <attractor@live.co.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.
- */
-
-/* This is a library for constructing the suffix array for a string containing
- * multiple sentinels with sentinels all represented by 0. The last symbol in
- * the string must be a sentinel. The library is modified from an early version
- * of Yuta Mori's SAIS library, but is slower than the lastest SAIS by about
- * 30%, partly due to the recent optimization Yuta has applied and partly due
- * to the extra comparisons between sentinels. This is not the first effort in
- * supporting multi-sentinel strings, but is probably the easiest to use. */
-
-#include <stdlib.h>
-
-#ifdef _KSA64
-#include <stdint.h>
-typedef int64_t saint_t;
-#define SAINT_MAX INT64_MAX
-#define SAIS_CORE ksa_core64
-#define SAIS_BWT ksa_bwt64
-#define SAIS_MAIN ksa_sa64
-#else
-#include <limits.h>
-typedef int saint_t;
-#define SAINT_MAX INT_MAX
-#define SAIS_CORE ksa_core
-#define SAIS_BWT ksa_bwt
-#define SAIS_MAIN ksa_sa
-#endif
-
-/* T is of type "const unsigned char*". If T[i] is a sentinel, chr(i) takes a negative value */
-#define chr(i) (cs == sizeof(saint_t) ? ((const saint_t *)T)[i] : (T[i]? (saint_t)T[i] : i - SAINT_MAX))
-
-/** Count the occurrences of each symbol */
-static void getCounts(const unsigned char *T, saint_t *C, saint_t n, saint_t k, int cs)
-{
- saint_t i;
- for (i = 0; i < k; ++i) C[i] = 0;
- for (i = 0; i < n; ++i) {
- saint_t c = chr(i);
- ++C[c > 0? c : 0];
- }
-}
-
-/**
- * Find the end of each bucket
- *
- * @param C occurrences computed by getCounts(); input
- * @param B start/end of each bucket; output
- * @param k size of alphabet
- * @param end compute the end of bucket if true; otherwise compute the end
- */
-static inline void getBuckets(const saint_t *C, saint_t *B, saint_t k, saint_t end)
-{
- saint_t i, sum = 0;
- if (end) for (i = 0; i < k; ++i) sum += C[i], B[i] = sum;
- else for (i = 0; i < k; ++i) sum += C[i], B[i] = sum - C[i];
-}
-
-/** Induced sort */
-static void induceSA(const unsigned char *T, saint_t *SA, saint_t *C, saint_t *B, saint_t n, saint_t k, saint_t cs)
-{
- saint_t *b, i, j;
- saint_t c0, c1;
- /* left-to-right induced sort (for L-type) */
- if (C == B) getCounts(T, C, n, k, cs);
- getBuckets(C, B, k, 0); /* find starts of buckets */
- for (i = 0, b = 0, c1 = -1; i < n; ++i) {
- j = SA[i], SA[i] = ~j;
- if (0 < j) { /* >0 if j-1 is L-type; <0 if S-type; ==0 undefined */
- --j;
- if ((c0 = chr(j)) != c1) {
- B[c1 > 0? c1 : 0] = b - SA;
- c1 = c0;
- b = SA + B[c1 > 0? c1 : 0];
- }
- *b++ = (0 < j && chr(j - 1) < c1) ? ~j : j;
- }
- }
- /* right-to-left induced sort (for S-type) */
- if (C == B) getCounts(T, C, n, k, cs);
- getBuckets(C, B, k, 1); /* find ends of buckets */
- for (i = n - 1, b = 0, c1 = -1; 0 <= i; --i) {
- if (0 < (j = SA[i])) { /* the prefix is S-type */
- --j;
- if ((c0 = chr(j)) != c1) {
- B[c1 > 0? c1 : 0] = b - SA;
- c1 = c0;
- b = SA + B[c1 > 0? c1 : 0];
- }
- if (c0 > 0) *--b = (j == 0 || chr(j - 1) > c1) ? ~j : j;
- } else SA[i] = ~j; /* if L-type, change the sign */
- }
-}
-
-/**
- * Recursively construct the suffix array for a string containing multiple
- * sentinels. NULL is taken as the sentinel.
- *
- * @param T NULL terminated input string (there can be multiple NULLs)
- * @param SA output suffix array
- * @param fs working space available in SA (typically 0 when first called)
- * @param n length of T, including the trailing NULL
- * @param k size of the alphabet (typically 256 when first called)
- * @param cs # bytes per element in T; 1 or sizeof(saint_t) (typically 1 when first called)
- *
- * @return 0 upon success
- */
-int SAIS_CORE(const unsigned char *T, saint_t *SA, saint_t fs, saint_t n, saint_t k, int cs)
-{
- saint_t *C, *B;
- saint_t i, j, c, m, q, qlen, name;
- saint_t c0, c1;
-
- /* STAGE I: reduce the problem by at least 1/2 sort all the S-substrings */
- if (k <= fs) C = SA + n, B = (k <= fs - k) ? C + k : C;
- else {
- if ((C = (saint_t*)malloc(k * (1 + (cs == 1)) * sizeof(saint_t))) == NULL) return -2;
- B = cs == 1? C + k : C;
- }
- getCounts(T, C, n, k, cs);
- getBuckets(C, B, k, 1); /* find ends of buckets */
- for (i = 0; i < n; ++i) SA[i] = 0;
- /* mark L and S (the t array in Nong et al.), and keep the positions of LMS in the buckets */
- for (i = n - 2, c = 1, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
- if ((c0 = chr(i)) < c1 + c) c = 1; /* c1 = chr(i+1); c==1 if in an S run */
- else if (c) SA[--B[c1 > 0? c1 : 0]] = i + 1, c = 0;
- }
- induceSA(T, SA, C, B, n, k, cs);
- if (fs < k) free(C);
- /* pack all the sorted LMS into the first m items of SA
- 2*m must be not larger than n (see Nong et al. for the proof) */
- for (i = 0, m = 0; i < n; ++i) {
- saint_t p = SA[i];
- if (p == n - 1) SA[m++] = p;
- else if (0 < p && chr(p - 1) > (c0 = chr(p))) {
- for (j = p + 1; j < n && c0 == (c1 = chr(j)); ++j);
- if (j < n && c0 < c1) SA[m++] = p;
- }
- }
- for (i = m; i < n; ++i) SA[i] = 0; /* init the name array buffer */
- /* store the length of all substrings */
- for (i = n - 2, j = n, c = 1, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
- if ((c0 = chr(i)) < c1 + c) c = 1; /* c1 = chr(i+1) */
- else if (c) SA[m + ((i + 1) >> 1)] = j - i - 1, j = i + 1, c = 0;
- }
- /* find the lexicographic names of all substrings */
- for (i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
- saint_t p = SA[i], plen = SA[m + (p >> 1)], diff = 1;
- if (plen == qlen) {
- for (j = 0; j < plen && chr(p + j) == chr(q + j); j++);
- if (j == plen) diff = 0;
- }
- if (diff) ++name, q = p, qlen = plen;
- SA[m + (p >> 1)] = name;
- }
-
- /* STAGE II: solve the reduced problem; recurse if names are not yet unique */
- if (name < m) {
- saint_t *RA = SA + n + fs - m - 1;
- for (i = n - 1, j = m - 1; m <= i; --i)
- if (SA[i] != 0) RA[j--] = SA[i];
- RA[m] = 0; // add a sentinel; in the resulting SA, SA[0]==m always stands
- if (SAIS_CORE((unsigned char *)RA, SA, fs + n - m * 2 - 2, m + 1, name + 1, sizeof(saint_t)) != 0) return -2;
- for (i = n - 2, j = m - 1, c = 1, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
- if ((c0 = chr(i)) < c1 + c) c = 1;
- else if (c) RA[j--] = i + 1, c = 0; /* get p1 */
- }
- for (i = 0; i < m; ++i) SA[i] = RA[SA[i+1]]; /* get index */
- }
-
- /* STAGE III: induce the result for the original problem */
- if (k <= fs) C = SA + n, B = (k <= fs - k) ? C + k : C;
- else {
- if ((C = (saint_t*)malloc(k * (1 + (cs == 1)) * sizeof(saint_t))) == NULL) return -2;
- B = cs == 1? C + k : C;
- }
- /* put all LMS characters into their buckets */
- getCounts(T, C, n, k, cs);
- getBuckets(C, B, k, 1); /* find ends of buckets */
- for (i = m; i < n; ++i) SA[i] = 0; /* init SA[m..n-1] */
- for (i = m - 1; 0 <= i; --i) {
- j = SA[i], SA[i] = 0;
- c = chr(j);
- SA[--B[c > 0? c : 0]] = j;
- }
- induceSA(T, SA, C, B, n, k, cs);
- if (fs < k) free(C);
- return 0;
-}
-
-/**
- * Construct the suffix array for a NULL terminated string possibly containing
- * multiple sentinels (NULLs).
- *
- * @param T[0..n-1] NULL terminated input string
- * @param SA[0..n-1] output suffix array
- * @param n length of the given string, including NULL
- * @param k size of the alphabet including the sentinel; no more than 256
- * @return 0 upon success
- */
-int SAIS_MAIN(const unsigned char *T, saint_t *SA, saint_t n, int k)
-{
- if (T == NULL || SA == NULL || T[n - 1] != '\0' || n <= 0) return -1;
- if (k < 0 || k > 256) k = 256;
- return SAIS_CORE(T, SA, 0, n, (saint_t)k, 1);
-}
-
-int SAIS_BWT(unsigned char *T, saint_t n, int k)
-{
- saint_t *SA, i;
- int ret;
- if ((SA = malloc(n * sizeof(saint_t))) == 0) return -1;
- if ((ret = SAIS_MAIN(T, SA, n, k)) != 0) return ret;
- for (i = 0; i < n; ++i)
- if (SA[i]) SA[i] = T[SA[i] - 1]; // if SA[i]==0, SA[i]=0
- for (i = 0; i < n; ++i) T[i] = SA[i];
- free(SA);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/kseq.h b/debian/vendor-h2o/deps/klib/kseq.h
deleted file mode 100644
index b2238d1..0000000
--- a/debian/vendor-h2o/deps/klib/kseq.h
+++ /dev/null
@@ -1,235 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.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.
-*/
-
-/* Last Modified: 05MAR2012 */
-
-#ifndef AC_KSEQ_H
-#define AC_KSEQ_H
-
-#include <ctype.h>
-#include <string.h>
-#include <stdlib.h>
-
-#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
-#define KS_SEP_TAB 1 // isspace() && !' '
-#define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows)
-#define KS_SEP_MAX 2
-
-#define __KS_TYPE(type_t) \
- typedef struct __kstream_t { \
- unsigned char *buf; \
- int begin, end, is_eof; \
- type_t f; \
- } kstream_t;
-
-#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
-#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
-
-#define __KS_BASIC(type_t, __bufsize) \
- static inline kstream_t *ks_init(type_t f) \
- { \
- kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
- ks->f = f; \
- ks->buf = (unsigned char*)malloc(__bufsize); \
- return ks; \
- } \
- static inline void ks_destroy(kstream_t *ks) \
- { \
- if (ks) { \
- free(ks->buf); \
- free(ks); \
- } \
- }
-
-#define __KS_GETC(__read, __bufsize) \
- static inline int ks_getc(kstream_t *ks) \
- { \
- if (ks->is_eof && ks->begin >= ks->end) return -1; \
- if (ks->begin >= ks->end) { \
- ks->begin = 0; \
- ks->end = __read(ks->f, ks->buf, __bufsize); \
- if (ks->end == 0) { ks->is_eof = 1; return -1;} \
- } \
- return (int)ks->buf[ks->begin++]; \
- }
-
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct __kstring_t {
- size_t l, m;
- char *s;
-} kstring_t;
-#endif
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-#define __KS_GETUNTIL(__read, __bufsize) \
- static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
- { \
- int gotany = 0; \
- if (dret) *dret = 0; \
- str->l = append? str->l : 0; \
- for (;;) { \
- int i; \
- if (ks->begin >= ks->end) { \
- if (!ks->is_eof) { \
- ks->begin = 0; \
- ks->end = __read(ks->f, ks->buf, __bufsize); \
- if (ks->end == 0) { ks->is_eof = 1; break; } \
- } else break; \
- } \
- if (delimiter == KS_SEP_LINE) { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (ks->buf[i] == '\n') break; \
- } else if (delimiter > KS_SEP_MAX) { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (ks->buf[i] == delimiter) break; \
- } else if (delimiter == KS_SEP_SPACE) { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (isspace(ks->buf[i])) break; \
- } else if (delimiter == KS_SEP_TAB) { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
- } else i = 0; /* never come to here! */ \
- if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \
- str->m = str->l + (i - ks->begin) + 1; \
- kroundup32(str->m); \
- str->s = (char*)realloc(str->s, str->m); \
- } \
- gotany = 1; \
- memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
- str->l = str->l + (i - ks->begin); \
- ks->begin = i + 1; \
- if (i < ks->end) { \
- if (dret) *dret = ks->buf[i]; \
- break; \
- } \
- } \
- if (!gotany && ks_eof(ks)) return -1; \
- if (str->s == 0) { \
- str->m = 1; \
- str->s = (char*)calloc(1, 1); \
- } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \
- str->s[str->l] = '\0'; \
- return str->l; \
- } \
- static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
- { return ks_getuntil2(ks, delimiter, str, dret, 0); }
-
-#define KSTREAM_INIT(type_t, __read, __bufsize) \
- __KS_TYPE(type_t) \
- __KS_BASIC(type_t, __bufsize) \
- __KS_GETC(__read, __bufsize) \
- __KS_GETUNTIL(__read, __bufsize)
-
-#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
-
-#define __KSEQ_BASIC(SCOPE, type_t) \
- SCOPE kseq_t *kseq_init(type_t fd) \
- { \
- kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
- s->f = ks_init(fd); \
- return s; \
- } \
- SCOPE void kseq_destroy(kseq_t *ks) \
- { \
- if (!ks) return; \
- free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
- ks_destroy(ks->f); \
- free(ks); \
- }
-
-/* Return value:
- >=0 length of the sequence (normal)
- -1 end-of-file
- -2 truncated quality string
- */
-#define __KSEQ_READ(SCOPE) \
- SCOPE int kseq_read(kseq_t *seq) \
- { \
- int c; \
- kstream_t *ks = seq->f; \
- if (seq->last_char == 0) { /* then jump to the next header line */ \
- while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
- if (c == -1) return -1; /* end of file */ \
- seq->last_char = c; \
- } /* else: the first header char has been read in the previous call */ \
- seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
- if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
- if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
- if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
- seq->seq.m = 256; \
- seq->seq.s = (char*)malloc(seq->seq.m); \
- } \
- while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
- if (c == '\n') continue; /* skip empty lines */ \
- seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
- ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
- } \
- if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
- if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
- seq->seq.m = seq->seq.l + 2; \
- kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
- seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
- } \
- seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
- if (c != '+') return seq->seq.l; /* FASTA */ \
- if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \
- seq->qual.m = seq->seq.m; \
- seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
- } \
- while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
- if (c == -1) return -2; /* error: no quality string */ \
- while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
- seq->last_char = 0; /* we have not come to the next header line */ \
- if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
- return seq->seq.l; \
- }
-
-#define __KSEQ_TYPE(type_t) \
- typedef struct { \
- kstring_t name, comment, seq, qual; \
- int last_char; \
- kstream_t *f; \
- } kseq_t;
-
-#define KSEQ_INIT2(SCOPE, type_t, __read) \
- KSTREAM_INIT(type_t, __read, 16384) \
- __KSEQ_TYPE(type_t) \
- __KSEQ_BASIC(SCOPE, type_t) \
- __KSEQ_READ(SCOPE)
-
-#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
-
-#define KSEQ_DECLARE(type_t) \
- __KS_TYPE(type_t) \
- __KSEQ_TYPE(type_t) \
- extern kseq_t *kseq_init(type_t fd); \
- void kseq_destroy(kseq_t *ks); \
- int kseq_read(kseq_t *seq);
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kson.c b/debian/vendor-h2o/deps/klib/kson.c
deleted file mode 100644
index a8bf160..0000000
--- a/debian/vendor-h2o/deps/klib/kson.c
+++ /dev/null
@@ -1,253 +0,0 @@
-#include <string.h>
-#include <stdlib.h>
-#include <stdarg.h>
-#include <assert.h>
-#include <ctype.h>
-#include <stdio.h>
-#include "kson.h"
-
-/*************
- *** Parse ***
- *************/
-
-kson_node_t *kson_parse_core(const char *json, long *_n, int *error, long *parsed_len)
-{
- long *stack = 0, top = 0, max = 0, n_a = 0, m_a = 0, i, j;
- kson_node_t *a = 0, *u;
- const char *p, *q;
- size_t *tmp;
-
-#define __push_back(y) do { \
- if (top == max) { \
- max = max? max<<1 : 4; \
- stack = (long*)realloc(stack, sizeof(long) * max); \
- } \
- stack[top++] = (y); \
- } while (0)
-
-#define __new_node(z) do { \
- if (n_a == m_a) { \
- long old_m = m_a; \
- m_a = m_a? m_a<<1 : 4; \
- a = (kson_node_t*)realloc(a, sizeof(kson_node_t) * m_a); \
- memset(a + old_m, 0, sizeof(kson_node_t) * (m_a - old_m)); \
- } \
- *(z) = &a[n_a++]; \
- } while (0)
-
- assert(sizeof(size_t) == sizeof(kson_node_t*));
- *error = KSON_OK;
- for (p = json; *p; ++p) {
- while (*p && isspace(*p)) ++p;
- if (*p == 0) break;
- if (*p == ',') { // comma is somewhat redundant
- } else if (*p == '[' || *p == '{') {
- int t = *p == '['? -1 : -2;
- if (top < 2 || stack[top-1] != -3) { // unnamed internal node
- __push_back(n_a);
- __new_node(&u);
- __push_back(t);
- } else stack[top-1] = t; // named internal node
- } else if (*p == ']' || *p == '}') {
- long i, start, t = *p == ']'? -1 : -2;
- for (i = top - 1; i >= 0 && stack[i] != t; --i);
- if (i < 0) { // error: an extra right bracket
- *error = KSON_ERR_EXTRA_RIGHT;
- break;
- }
- start = i;
- u = &a[stack[start-1]];
- u->key = u->v.str;
- u->n = top - 1 - start;
- u->v.child = (kson_node_t**)malloc(u->n * sizeof(kson_node_t*));
- tmp = (size_t*)u->v.child;
- for (i = start + 1; i < top; ++i)
- tmp[i - start - 1] = stack[i];
- u->type = *p == ']'? KSON_TYPE_BRACKET : KSON_TYPE_BRACE;
- if ((top = start) == 1) break; // completed one object; remaining characters discarded
- } else if (*p == ':') {
- if (top == 0 || stack[top-1] == -3) {
- *error = KSON_ERR_NO_KEY;
- break;
- }
- __push_back(-3);
- } else {
- int c = *p;
- // get the node to modify
- if (top >= 2 && stack[top-1] == -3) { // we have a key:value pair here
- --top;
- u = &a[stack[top-1]];
- u->key = u->v.str; // move old value to key
- } else { // don't know if this is a bare value or a key:value pair; keep it as a value for now
- __push_back(n_a);
- __new_node(&u);
- }
- // parse string
- if (c == '\'' || c == '"') {
- for (q = ++p; *q && *q != c; ++q)
- if (*q == '\\') ++q;
- } else {
- for (q = p; *q && *q != ']' && *q != '}' && *q != ',' && *q != ':' && *q != '\n'; ++q)
- if (*q == '\\') ++q;
- }
- u->v.str = (char*)malloc(q - p + 1); strncpy(u->v.str, p, q - p); u->v.str[q-p] = 0; // equivalent to u->v.str=strndup(p, q-p)
- u->type = c == '\''? KSON_TYPE_SGL_QUOTE : c == '"'? KSON_TYPE_DBL_QUOTE : KSON_TYPE_NO_QUOTE;
- p = c == '\'' || c == '"'? q : q - 1;
- }
- }
- while (*p && isspace(*p)) ++p; // skip trailing blanks
- if (parsed_len) *parsed_len = p - json;
- if (top != 1) *error = KSON_ERR_EXTRA_LEFT;
-
- for (i = 0; i < n_a; ++i)
- for (j = 0, u = &a[i], tmp = (size_t*)u->v.child; j < (long)u->n; ++j)
- u->v.child[j] = &a[tmp[j]];
-
- free(stack);
- *_n = n_a;
- return a;
-}
-
-void kson_destroy(kson_t *kson)
-{
- long i;
- if (kson == 0) return;
- for (i = 0; i < kson->n_nodes; ++i) {
- free(kson->root[i].key); free(kson->root[i].v.str);
- }
- free(kson->root); free(kson);
-}
-
-kson_t *kson_parse(const char *json)
-{
- kson_t *kson;
- int error;
- kson = (kson_t*)calloc(1, sizeof(kson_t));
- kson->root = kson_parse_core(json, &kson->n_nodes, &error, 0);
- if (error) {
- kson_destroy(kson);
- return 0;
- }
- return kson;
-}
-
-/*************
- *** Query ***
- *************/
-
-const kson_node_t *kson_by_path(const kson_node_t *p, int depth, ...)
-{
- va_list ap;
- va_start(ap, depth);
- while (p && depth > 0) {
- if (p->type == KSON_TYPE_BRACE) {
- p = kson_by_key(p, va_arg(ap, const char*));
- } else if (p->type == KSON_TYPE_BRACKET) {
- p = kson_by_index(p, va_arg(ap, long));
- } else break;
- --depth;
- }
- va_end(ap);
- return p;
-}
-
-/**************
- *** Fromat ***
- **************/
-
-void kson_format_recur(const kson_node_t *p, int depth)
-{
- long i;
- if (p->key) printf("\"%s\":", p->key);
- if (p->type == KSON_TYPE_BRACKET || p->type == KSON_TYPE_BRACE) {
- putchar(p->type == KSON_TYPE_BRACKET? '[' : '{');
- if (p->n) {
- putchar('\n'); for (i = 0; i <= depth; ++i) fputs(" ", stdout);
- for (i = 0; i < (long)p->n; ++i) {
- if (i) {
- int i;
- putchar(',');
- putchar('\n'); for (i = 0; i <= depth; ++i) fputs(" ", stdout);
- }
- kson_format_recur(p->v.child[i], depth + 1);
- }
- putchar('\n'); for (i = 0; i < depth; ++i) fputs(" ", stdout);
- }
- putchar(p->type == KSON_TYPE_BRACKET? ']' : '}');
- } else {
- if (p->type != KSON_TYPE_NO_QUOTE)
- putchar(p->type == KSON_TYPE_SGL_QUOTE? '\'' : '"');
- fputs(p->v.str, stdout);
- if (p->type != KSON_TYPE_NO_QUOTE)
- putchar(p->type == KSON_TYPE_SGL_QUOTE? '\'' : '"');
- }
-}
-
-void kson_format(const kson_node_t *root)
-{
- kson_format_recur(root, 0);
- putchar('\n');
-}
-
-/*********************
- *** Main function ***
- *********************/
-
-#ifdef KSON_MAIN
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-int main(int argc, char *argv[])
-{
- kson_t *kson = 0;
- if (argc > 1) {
- FILE *fp;
- int len = 0, max = 0, tmp, i;
- char *json = 0, buf[0x10000];
- if ((fp = fopen(argv[1], "rb")) != 0) {
- // read the entire file into a string
- while ((tmp = fread(buf, 1, 0x10000, fp)) != 0) {
- if (len + tmp + 1 > max) {
- max = len + tmp + 1;
- kroundup32(max);
- json = (char*)realloc(json, max);
- }
- memcpy(json + len, buf, tmp);
- len += tmp;
- }
- fclose(fp);
- // parse
- kson = kson_parse(json);
- free(json);
- if (kson) {
- kson_format(kson->root);
- if (argc > 2) {
- // path finding
- const kson_node_t *p = kson->root;
- for (i = 2; i < argc && p; ++i) {
- if (p->type == KSON_TYPE_BRACKET)
- p = kson_by_index(p, atoi(argv[i]));
- else if (p->type == KSON_TYPE_BRACE)
- p = kson_by_key(p, argv[i]);
- else p = 0;
- }
- if (p) {
- if (kson_is_internal(p)) printf("Reached an internal node\n");
- else printf("Value: %s\n", p->v.str);
- } else printf("Failed to find the slot\n");
- }
- } else printf("Failed to parse\n");
- }
- } else {
- kson = kson_parse("{'a' : 1,'b':[0,'isn\\'t',true],'d':[{\n\n\n}]}");
- if (kson) {
- const kson_node_t *p = kson_by_path(kson->root, 2, "b", 1);
- if (p) printf("*** %s\n", p->v.str);
- else printf("!!! not found\n");
- kson_format(kson->root);
- } else {
- printf("Failed to parse\n");
- }
- }
- kson_destroy(kson);
- return 0;
-}
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kson.h b/debian/vendor-h2o/deps/klib/kson.h
deleted file mode 100644
index a03eb52..0000000
--- a/debian/vendor-h2o/deps/klib/kson.h
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef KSON_H
-#define KSON_H
-
-#include <string.h>
-
-#define KSON_TYPE_NO_QUOTE 1
-#define KSON_TYPE_SGL_QUOTE 2
-#define KSON_TYPE_DBL_QUOTE 3
-#define KSON_TYPE_BRACKET 4
-#define KSON_TYPE_BRACE 5
-
-#define KSON_OK 0
-#define KSON_ERR_EXTRA_LEFT 1
-#define KSON_ERR_EXTRA_RIGHT 2
-#define KSON_ERR_NO_KEY 3
-
-typedef struct kson_node_s {
- unsigned long long type:3, n:61;
- char *key;
- union {
- struct kson_node_s **child;
- char *str;
- } v;
-} kson_node_t;
-
-typedef struct {
- long n_nodes;
- kson_node_t *root;
-} kson_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- kson_t *kson_parse(const char *json);
- void kson_destroy(kson_t *kson);
- const kson_node_t *kson_by_path(const kson_node_t *root, int path_len, ...);
- void kson_format(const kson_node_t *root);
-
-#ifdef __cplusplus
-}
-#endif
-
-#define kson_is_internal(p) ((p)->type == KSON_TYPE_BRACKET || (p)->type == KSON_TYPE_BRACE)
-
-static inline const kson_node_t *kson_by_key(const kson_node_t *p, const char *key)
-{
- long i;
- if (!kson_is_internal(p)) return 0;
- for (i = 0; i < (long)p->n; ++i) {
- const kson_node_t *q = p->v.child[i];
- if (q->key && strcmp(q->key, key) == 0)
- return q;
- }
- return 0;
-}
-
-static inline const kson_node_t *kson_by_index(const kson_node_t *p, long i)
-{
- if (!kson_is_internal(p)) return 0;
- return 0 <= i && i < (long)p->n? p->v.child[i] : 0;
-}
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/ksort.h b/debian/vendor-h2o/deps/klib/ksort.h
deleted file mode 100644
index 4da7a13..0000000
--- a/debian/vendor-h2o/deps/klib/ksort.h
+++ /dev/null
@@ -1,298 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008, 2011 Attractive Chaos <attractor@live.co.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.
-*/
-
-/*
- 2011-04-10 (0.1.6):
-
- * Added sample
-
- 2011-03 (0.1.5):
-
- * Added shuffle/permutation
-
- 2008-11-16 (0.1.4):
-
- * Fixed a bug in introsort() that happens in rare cases.
-
- 2008-11-05 (0.1.3):
-
- * Fixed a bug in introsort() for complex comparisons.
-
- * Fixed a bug in mergesort(). The previous version is not stable.
-
- 2008-09-15 (0.1.2):
-
- * Accelerated introsort. On my Mac (not on another Linux machine),
- my implementation is as fast as std::sort on random input.
-
- * Added combsort and in introsort, switch to combsort if the
- recursion is too deep.
-
- 2008-09-13 (0.1.1):
-
- * Added k-small algorithm
-
- 2008-09-05 (0.1.0):
-
- * Initial version
-
-*/
-
-#ifndef AC_KSORT_H
-#define AC_KSORT_H
-
-#include <stdlib.h>
-#include <string.h>
-
-typedef struct {
- void *left, *right;
- int depth;
-} ks_isort_stack_t;
-
-#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
-
-#define KSORT_INIT(name, type_t, __sort_lt) \
- void ks_mergesort_##name(size_t n, type_t array[], type_t temp[]) \
- { \
- type_t *a2[2], *a, *b; \
- int curr, shift; \
- \
- a2[0] = array; \
- a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n); \
- for (curr = 0, shift = 0; (1ul<<shift) < n; ++shift) { \
- a = a2[curr]; b = a2[1-curr]; \
- if (shift == 0) { \
- type_t *p = b, *i, *eb = a + n; \
- for (i = a; i < eb; i += 2) { \
- if (i == eb - 1) *p++ = *i; \
- else { \
- if (__sort_lt(*(i+1), *i)) { \
- *p++ = *(i+1); *p++ = *i; \
- } else { \
- *p++ = *i; *p++ = *(i+1); \
- } \
- } \
- } \
- } else { \
- size_t i, step = 1ul<<shift; \
- for (i = 0; i < n; i += step<<1) { \
- type_t *p, *j, *k, *ea, *eb; \
- if (n < i + step) { \
- ea = a + n; eb = a; \
- } else { \
- ea = a + i + step; \
- eb = a + (n < i + (step<<1)? n : i + (step<<1)); \
- } \
- j = a + i; k = a + i + step; p = b + i; \
- while (j < ea && k < eb) { \
- if (__sort_lt(*k, *j)) *p++ = *k++; \
- else *p++ = *j++; \
- } \
- while (j < ea) *p++ = *j++; \
- while (k < eb) *p++ = *k++; \
- } \
- } \
- curr = 1 - curr; \
- } \
- if (curr == 1) { \
- type_t *p = a2[0], *i = a2[1], *eb = array + n; \
- for (; p < eb; ++i) *p++ = *i; \
- } \
- if (temp == 0) free(a2[1]); \
- } \
- void ks_heapadjust_##name(size_t i, size_t n, type_t l[]) \
- { \
- size_t k = i; \
- type_t tmp = l[i]; \
- while ((k = (k << 1) + 1) < n) { \
- if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k; \
- if (__sort_lt(l[k], tmp)) break; \
- l[i] = l[k]; i = k; \
- } \
- l[i] = tmp; \
- } \
- void ks_heapmake_##name(size_t lsize, type_t l[]) \
- { \
- size_t i; \
- for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i) \
- ks_heapadjust_##name(i, lsize, l); \
- } \
- void ks_heapsort_##name(size_t lsize, type_t l[]) \
- { \
- size_t i; \
- for (i = lsize - 1; i > 0; --i) { \
- type_t tmp; \
- tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
- } \
- } \
- static inline void __ks_insertsort_##name(type_t *s, type_t *t) \
- { \
- type_t *i, *j, swap_tmp; \
- for (i = s + 1; i < t; ++i) \
- for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \
- swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp; \
- } \
- } \
- void ks_combsort_##name(size_t n, type_t a[]) \
- { \
- const double shrink_factor = 1.2473309501039786540366528676643; \
- int do_swap; \
- size_t gap = n; \
- type_t tmp, *i, *j; \
- do { \
- if (gap > 2) { \
- gap = (size_t)(gap / shrink_factor); \
- if (gap == 9 || gap == 10) gap = 11; \
- } \
- do_swap = 0; \
- for (i = a; i < a + n - gap; ++i) { \
- j = i + gap; \
- if (__sort_lt(*j, *i)) { \
- tmp = *i; *i = *j; *j = tmp; \
- do_swap = 1; \
- } \
- } \
- } while (do_swap || gap > 2); \
- if (gap != 1) __ks_insertsort_##name(a, a + n); \
- } \
- void ks_introsort_##name(size_t n, type_t a[]) \
- { \
- int d; \
- ks_isort_stack_t *top, *stack; \
- type_t rp, swap_tmp; \
- type_t *s, *t, *i, *j, *k; \
- \
- if (n < 1) return; \
- else if (n == 2) { \
- if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
- return; \
- } \
- for (d = 2; 1ul<<d < n; ++d); \
- stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
- top = stack; s = a; t = a + (n-1); d <<= 1; \
- while (1) { \
- if (s < t) { \
- if (--d == 0) { \
- ks_combsort_##name(t - s + 1, s); \
- t = s; \
- continue; \
- } \
- i = s; j = t; k = i + ((j-i)>>1) + 1; \
- if (__sort_lt(*k, *i)) { \
- if (__sort_lt(*k, *j)) k = j; \
- } else k = __sort_lt(*j, *i)? i : j; \
- rp = *k; \
- if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; } \
- for (;;) { \
- do ++i; while (__sort_lt(*i, rp)); \
- do --j; while (i <= j && __sort_lt(rp, *j)); \
- if (j <= i) break; \
- swap_tmp = *i; *i = *j; *j = swap_tmp; \
- } \
- swap_tmp = *i; *i = *t; *t = swap_tmp; \
- if (i-s > t-i) { \
- if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
- s = t-i > 16? i+1 : t; \
- } else { \
- if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
- t = i-s > 16? i-1 : s; \
- } \
- } else { \
- if (top == stack) { \
- free(stack); \
- __ks_insertsort_##name(a, a+n); \
- return; \
- } else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
- } \
- } \
- } \
- /* This function is adapted from: http://ndevilla.free.fr/median/ */ \
- /* 0 <= kk < n */ \
- type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk) \
- { \
- type_t *low, *high, *k, *ll, *hh, *mid; \
- low = arr; high = arr + n - 1; k = arr + kk; \
- for (;;) { \
- if (high <= low) return *k; \
- if (high == low + 1) { \
- if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
- return *k; \
- } \
- mid = low + (high - low) / 2; \
- if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
- if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
- if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \
- KSORT_SWAP(type_t, *mid, *(low+1)); \
- ll = low + 1; hh = high; \
- for (;;) { \
- do ++ll; while (__sort_lt(*ll, *low)); \
- do --hh; while (__sort_lt(*low, *hh)); \
- if (hh < ll) break; \
- KSORT_SWAP(type_t, *ll, *hh); \
- } \
- KSORT_SWAP(type_t, *low, *hh); \
- if (hh <= k) low = ll; \
- if (hh >= k) high = hh - 1; \
- } \
- } \
- void ks_shuffle_##name(size_t n, type_t a[]) \
- { \
- int i, j; \
- for (i = n; i > 1; --i) { \
- type_t tmp; \
- j = (int)(drand48() * i); \
- tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp; \
- } \
- } \
- void ks_sample_##name(size_t n, size_t r, type_t a[]) /* FIXME: NOT TESTED!!! */ \
- { /* reference: http://code.activestate.com/recipes/272884/ */ \
- int i, k, pop = n; \
- for (i = (int)r, k = 0; i >= 0; --i) { \
- double z = 1., x = drand48(); \
- type_t tmp; \
- while (x < z) z -= z * i / (pop--); \
- if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \
- ++k; \
- } \
- }
-
-#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
-#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
-#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
-#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
-#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
-#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
-#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
-#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a)
-
-#define ks_lt_generic(a, b) ((a) < (b))
-#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)
-
-typedef const char *ksstr_t;
-
-#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
-#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kstring.c b/debian/vendor-h2o/deps/klib/kstring.c
deleted file mode 100644
index f029317..0000000
--- a/debian/vendor-h2o/deps/klib/kstring.c
+++ /dev/null
@@ -1,229 +0,0 @@
-#include <stdarg.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <string.h>
-#include <stdint.h>
-#include "kstring.h"
-
-int kvsprintf(kstring_t *s, const char *fmt, va_list ap)
-{
- va_list args;
- int l;
- va_copy(args, ap);
- l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); // This line does not work with glibc 2.0. See `man snprintf'.
- va_end(args);
- if (l + 1 > s->m - s->l) {
- s->m = s->l + l + 2;
- kroundup32(s->m);
- s->s = (char*)realloc(s->s, s->m);
- va_copy(args, ap);
- l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args);
- va_end(args);
- }
- s->l += l;
- return l;
-}
-
-int ksprintf(kstring_t *s, const char *fmt, ...)
-{
- va_list ap;
- int l;
- va_start(ap, fmt);
- l = kvsprintf(s, fmt, ap);
- va_end(ap);
- return l;
-}
-
-char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux)
-{
- const char *p, *start;
- if (sep) { // set up the table
- if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished
- aux->finished = 0;
- if (sep[1]) {
- aux->sep = -1;
- aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
- for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f);
- } else aux->sep = sep[0];
- }
- if (aux->finished) return 0;
- else if (str) aux->p = str - 1, aux->finished = 0;
- if (aux->sep < 0) {
- for (p = start = aux->p + 1; *p; ++p)
- if (aux->tab[*p>>6]>>(*p&0x3f)&1) break;
- } else {
- for (p = start = aux->p + 1; *p; ++p)
- if (*p == aux->sep) break;
- }
- aux->p = p; // end of token
- if (*p == 0) aux->finished = 1; // no more tokens
- return (char*)start;
-}
-
-// s MUST BE a null terminated string; l = strlen(s)
-int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
-{
- int i, n, max, last_char, last_start, *offsets, l;
- n = 0; max = *_max; offsets = *_offsets;
- l = strlen(s);
-
-#define __ksplit_aux do { \
- if (_offsets) { \
- s[i] = 0; \
- if (n == max) { \
- int *tmp; \
- max = max? max<<1 : 2; \
- if ((tmp = (int*)realloc(offsets, sizeof(int) * max))) { \
- offsets = tmp; \
- } else { \
- free(offsets); \
- *_offsets = NULL; \
- return 0; \
- } \
- } \
- offsets[n++] = last_start; \
- } else ++n; \
- } while (0)
-
- for (i = 0, last_char = last_start = 0; i <= l; ++i) {
- if (delimiter == 0) {
- if (isspace(s[i]) || s[i] == 0) {
- if (isgraph(last_char)) __ksplit_aux; // the end of a field
- } else {
- if (isspace(last_char) || last_char == 0) last_start = i;
- }
- } else {
- if (s[i] == delimiter || s[i] == 0) {
- if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field
- } else {
- if (last_char == delimiter || last_char == 0) last_start = i;
- }
- }
- last_char = s[i];
- }
- *_max = max; *_offsets = offsets;
- return n;
-}
-
-/**********************
- * Boyer-Moore search *
- **********************/
-
-typedef unsigned char ubyte_t;
-
-// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
-static int *ksBM_prep(const ubyte_t *pat, int m)
-{
- int i, *suff, *prep, *bmGs, *bmBc;
- prep = (int*)calloc(m + 256, sizeof(int));
- bmGs = prep; bmBc = prep + m;
- { // preBmBc()
- for (i = 0; i < 256; ++i) bmBc[i] = m;
- for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
- }
- suff = (int*)calloc(m, sizeof(int));
- { // suffixes()
- int f = 0, g;
- suff[m - 1] = m;
- g = m - 1;
- for (i = m - 2; i >= 0; --i) {
- if (i > g && suff[i + m - 1 - f] < i - g)
- suff[i] = suff[i + m - 1 - f];
- else {
- if (i < g) g = i;
- f = i;
- while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g;
- suff[i] = f - g;
- }
- }
- }
- { // preBmGs()
- int j = 0;
- for (i = 0; i < m; ++i) bmGs[i] = m;
- for (i = m - 1; i >= 0; --i)
- if (suff[i] == i + 1)
- for (; j < m - 1 - i; ++j)
- if (bmGs[j] == m)
- bmGs[j] = m - 1 - i;
- for (i = 0; i <= m - 2; ++i)
- bmGs[m - 1 - suff[i]] = m - 1 - i;
- }
- free(suff);
- return prep;
-}
-
-void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep)
-{
- int i, j, *prep = 0, *bmGs, *bmBc;
- const ubyte_t *str, *pat;
- str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat;
- prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep;
- if (_prep && *_prep == 0) *_prep = prep;
- bmGs = prep; bmBc = prep + m;
- j = 0;
- while (j <= n - m) {
- for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i);
- if (i >= 0) {
- int max = bmBc[str[i+j]] - m + 1 + i;
- if (max < bmGs[i]) max = bmGs[i];
- j += max;
- } else return (void*)(str + j);
- }
- if (_prep == 0) free(prep);
- return 0;
-}
-
-char *kstrstr(const char *str, const char *pat, int **_prep)
-{
- return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
-}
-
-char *kstrnstr(const char *str, const char *pat, int n, int **_prep)
-{
- return (char*)kmemmem(str, n, pat, strlen(pat), _prep);
-}
-
-/***********************
- * The main() function *
- ***********************/
-
-#ifdef KSTRING_MAIN
-#include <stdio.h>
-int main()
-{
- kstring_t *s;
- int *fields, n, i;
- ks_tokaux_t aux;
- char *p;
- s = (kstring_t*)calloc(1, sizeof(kstring_t));
- // test ksprintf()
- ksprintf(s, " abcdefg: %d ", 100);
- printf("'%s'\n", s->s);
- // test ksplit()
- fields = ksplit(s, 0, &n);
- for (i = 0; i < n; ++i)
- printf("field[%d] = '%s'\n", i, s->s + fields[i]);
- // test kstrtok()
- s->l = 0;
- for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) {
- kputsn(p, aux.p - p, s);
- kputc('\n', s);
- }
- printf("%s", s->s);
- // free
- free(s->s); free(s); free(fields);
-
- {
- static char *str = "abcdefgcdgcagtcakcdcd";
- static char *pat = "cd";
- char *ret, *s = str;
- int *prep = 0;
- while ((ret = kstrstr(s, pat, &prep)) != 0) {
- printf("match: %s\n", ret);
- s = ret + prep[0];
- }
- free(prep);
- }
- return 0;
-}
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kstring.h b/debian/vendor-h2o/deps/klib/kstring.h
deleted file mode 100644
index 0e654cb..0000000
--- a/debian/vendor-h2o/deps/klib/kstring.h
+++ /dev/null
@@ -1,259 +0,0 @@
-/* The MIT License
-
- Copyright (c) by Attractive Chaos <attractor@live.co.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 KSTRING_H
-#define KSTRING_H
-
-#include <stdlib.h>
-#include <string.h>
-#include <stdarg.h>
-#include <stdint.h>
-#include <stdio.h>
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ > 4)
-#define KS_ATTR_PRINTF(fmt, arg) __attribute__((__format__ (__printf__, fmt, arg)))
-#else
-#define KS_ATTR_PRINTF(fmt, arg)
-#endif
-
-
-/* kstring_t is a simple non-opaque type whose fields are likely to be
- * used directly by user code (but see also ks_str() and ks_len() below).
- * A kstring_t object is initialised by either of
- * kstring_t str = { 0, 0, NULL };
- * kstring_t str; ...; str.l = str.m = 0; str.s = NULL;
- * and either ownership of the underlying buffer should be given away before
- * the object disappears (i.e., the str.s pointer copied and something else
- * responsible for freeing it), or the kstring_t should be destroyed with
- * free(str.s); */
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct __kstring_t {
- size_t l, m;
- char *s;
-} kstring_t;
-#endif
-
-typedef struct {
- uint64_t tab[4];
- int sep, finished;
- const char *p; // end of the current token
-} ks_tokaux_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- int kvsprintf(kstring_t *s, const char *fmt, va_list ap) KS_ATTR_PRINTF(2,0);
- int ksprintf(kstring_t *s, const char *fmt, ...) KS_ATTR_PRINTF(2,3);
- int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
- char *kstrstr(const char *str, const char *pat, int **_prep);
- char *kstrnstr(const char *str, const char *pat, int n, int **_prep);
- void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep);
-
- /* kstrtok() is similar to strtok_r() except that str is not
- * modified and both str and sep can be NULL. For efficiency, it is
- * actually recommended to set both to NULL in the subsequent calls
- * if sep is not changed. */
- char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux);
-
-#ifdef __cplusplus
-}
-#endif
-
-static inline int ks_resize(kstring_t *s, size_t size)
-{
- if (s->m < size) {
- char *tmp;
- s->m = size;
- kroundup32(s->m);
- if ((tmp = (char*)realloc(s->s, s->m)))
- s->s = tmp;
- else
- return -1;
- }
- return 0;
-}
-
-static inline char *ks_str(kstring_t *s)
-{
- return s->s;
-}
-
-static inline size_t ks_len(kstring_t *s)
-{
- return s->l;
-}
-
-static inline int kputsn(const char *p, int l, kstring_t *s)
-{
- if (s->l + l + 1 >= s->m) {
- char *tmp;
- s->m = s->l + l + 2;
- kroundup32(s->m);
- if ((tmp = (char*)realloc(s->s, s->m)))
- s->s = tmp;
- else
- return EOF;
- }
- memcpy(s->s + s->l, p, l);
- s->l += l;
- s->s[s->l] = 0;
- return l;
-}
-
-static inline int kputs(const char *p, kstring_t *s)
-{
- return kputsn(p, strlen(p), s);
-}
-
-static inline int kputc(int c, kstring_t *s)
-{
- if (s->l + 1 >= s->m) {
- char *tmp;
- s->m = s->l + 2;
- kroundup32(s->m);
- if ((tmp = (char*)realloc(s->s, s->m)))
- s->s = tmp;
- else
- return EOF;
- }
- s->s[s->l++] = c;
- s->s[s->l] = 0;
- return c;
-}
-
-static inline int kputc_(int c, kstring_t *s)
-{
- if (s->l + 1 > s->m) {
- char *tmp;
- s->m = s->l + 1;
- kroundup32(s->m);
- if ((tmp = (char*)realloc(s->s, s->m)))
- s->s = tmp;
- else
- return EOF;
- }
- s->s[s->l++] = c;
- return 1;
-}
-
-static inline int kputsn_(const void *p, int l, kstring_t *s)
-{
- if (s->l + l > s->m) {
- char *tmp;
- s->m = s->l + l;
- kroundup32(s->m);
- if ((tmp = (char*)realloc(s->s, s->m)))
- s->s = tmp;
- else
- return EOF;
- }
- memcpy(s->s + s->l, p, l);
- s->l += l;
- return l;
-}
-
-static inline int kputw(int c, kstring_t *s)
-{
- char buf[16];
- int i, l = 0;
- unsigned int x = c;
- if (c < 0) x = -x;
- do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);
- if (c < 0) buf[l++] = '-';
- if (s->l + l + 1 >= s->m) {
- char *tmp;
- s->m = s->l + l + 2;
- kroundup32(s->m);
- if ((tmp = (char*)realloc(s->s, s->m)))
- s->s = tmp;
- else
- return EOF;
- }
- for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
- s->s[s->l] = 0;
- return 0;
-}
-
-static inline int kputuw(unsigned c, kstring_t *s)
-{
- char buf[16];
- int l, i;
- unsigned x;
- if (c == 0) return kputc('0', s);
- for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
- if (s->l + l + 1 >= s->m) {
- char *tmp;
- s->m = s->l + l + 2;
- kroundup32(s->m);
- if ((tmp = (char*)realloc(s->s, s->m)))
- s->s = tmp;
- else
- return EOF;
- }
- for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
- s->s[s->l] = 0;
- return 0;
-}
-
-static inline int kputl(long c, kstring_t *s)
-{
- char buf[32];
- int i, l = 0;
- unsigned long x = c;
- if (c < 0) x = -x;
- do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);
- if (c < 0) buf[l++] = '-';
- if (s->l + l + 1 >= s->m) {
- char *tmp;
- s->m = s->l + l + 2;
- kroundup32(s->m);
- if ((tmp = (char*)realloc(s->s, s->m)))
- s->s = tmp;
- else
- return EOF;
- }
- for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
- s->s[s->l] = 0;
- return 0;
-}
-
-/*
- * Returns 's' split by delimiter, with *n being the number of components;
- * NULL on failue.
- */
-static inline int *ksplit(kstring_t *s, int delimiter, int *n)
-{
- int max = 0, *offsets = 0;
- *n = ksplit_core(s->s, delimiter, &max, &offsets);
- return offsets;
-}
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/ksw.c b/debian/vendor-h2o/deps/klib/ksw.c
deleted file mode 100644
index 742fec9..0000000
--- a/debian/vendor-h2o/deps/klib/ksw.c
+++ /dev/null
@@ -1,633 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2011 by Attractive Chaos <attractor@live.co.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.
-*/
-
-#include <stdlib.h>
-#include <stdint.h>
-#include <emmintrin.h>
-#include "ksw.h"
-
-#ifdef __GNUC__
-#define LIKELY(x) __builtin_expect((x),1)
-#define UNLIKELY(x) __builtin_expect((x),0)
-#else
-#define LIKELY(x) (x)
-#define UNLIKELY(x) (x)
-#endif
-
-const kswr_t g_defr = { 0, -1, -1, -1, -1, -1, -1 };
-
-struct _kswq_t {
- int qlen, slen;
- uint8_t shift, mdiff, max, size;
- __m128i *qp, *H0, *H1, *E, *Hmax;
-};
-
-/**
- * Initialize the query data structure
- *
- * @param size Number of bytes used to store a score; valid valures are 1 or 2
- * @param qlen Length of the query sequence
- * @param query Query sequence
- * @param m Size of the alphabet
- * @param mat Scoring matrix in a one-dimension array
- *
- * @return Query data structure
- */
-kswq_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const int8_t *mat)
-{
- kswq_t *q;
- int slen, a, tmp, p;
-
- size = size > 1? 2 : 1;
- p = 8 * (3 - size); // # values per __m128i
- slen = (qlen + p - 1) / p; // segmented length
- q = (kswq_t*)malloc(sizeof(kswq_t) + 256 + 16 * slen * (m + 4)); // a single block of memory
- q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory
- q->H0 = q->qp + slen * m;
- q->H1 = q->H0 + slen;
- q->E = q->H1 + slen;
- q->Hmax = q->E + slen;
- q->slen = slen; q->qlen = qlen; q->size = size;
- // compute shift
- tmp = m * m;
- for (a = 0, q->shift = 127, q->mdiff = 0; a < tmp; ++a) { // find the minimum and maximum score
- if (mat[a] < (int8_t)q->shift) q->shift = mat[a];
- if (mat[a] > (int8_t)q->mdiff) q->mdiff = mat[a];
- }
- q->max = q->mdiff;
- q->shift = 256 - q->shift; // NB: q->shift is uint8_t
- q->mdiff += q->shift; // this is the difference between the min and max scores
- // An example: p=8, qlen=19, slen=3 and segmentation:
- // {{0,3,6,9,12,15,18,-1},{1,4,7,10,13,16,-1,-1},{2,5,8,11,14,17,-1,-1}}
- if (size == 1) {
- int8_t *t = (int8_t*)q->qp;
- for (a = 0; a < m; ++a) {
- int i, k, nlen = slen * p;
- const int8_t *ma = mat + a * m;
- for (i = 0; i < slen; ++i)
- for (k = i; k < nlen; k += slen) // p iterations
- *t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
- }
- } else {
- int16_t *t = (int16_t*)q->qp;
- for (a = 0; a < m; ++a) {
- int i, k, nlen = slen * p;
- const int8_t *ma = mat + a * m;
- for (i = 0; i < slen; ++i)
- for (k = i; k < nlen; k += slen) // p iterations
- *t++ = (k >= qlen? 0 : ma[query[k]]);
- }
- }
- return q;
-}
-
-kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra) // the first gap costs -(_o+_e)
-{
- int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
- uint64_t *b;
- __m128i zero, gapoe, gape, shift, *H0, *H1, *E, *Hmax;
- kswr_t r;
-
-#define __max_16(ret, xx) do { \
- (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \
- (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 4)); \
- (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 2)); \
- (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 1)); \
- (ret) = _mm_extract_epi16((xx), 0) & 0x00ff; \
- } while (0)
-
- // initialization
- r = g_defr;
- minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
- endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
- m_b = n_b = 0; b = 0;
- zero = _mm_set1_epi32(0);
- gapoe = _mm_set1_epi8(_gapo + _gape);
- gape = _mm_set1_epi8(_gape);
- shift = _mm_set1_epi8(q->shift);
- H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
- slen = q->slen;
- for (i = 0; i < slen; ++i) {
- _mm_store_si128(E + i, zero);
- _mm_store_si128(H0 + i, zero);
- _mm_store_si128(Hmax + i, zero);
- }
- // the core loop
- for (i = 0; i < tlen; ++i) {
- int j, k, cmp, imax;
- __m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
- h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
- h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian
- for (j = 0; LIKELY(j < slen); ++j) {
- /* SW cells are computed in the following order:
- * H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
- * E(i+1,j) = max{H(i,j)-q, E(i,j)-r}
- * F(i,j+1) = max{H(i,j)-q, F(i,j)-r}
- */
- // compute H'(i,j); note that at the beginning, h=H'(i-1,j-1)
- h = _mm_adds_epu8(h, _mm_load_si128(S + j));
- h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)
- e = _mm_load_si128(E + j); // e=E'(i,j)
- h = _mm_max_epu8(h, e);
- h = _mm_max_epu8(h, f); // h=H'(i,j)
- max = _mm_max_epu8(max, h); // set max
- _mm_store_si128(H1 + j, h); // save to H'(i,j)
- // now compute E'(i+1,j)
- h = _mm_subs_epu8(h, gapoe); // h=H'(i,j)-gapo
- e = _mm_subs_epu8(e, gape); // e=E'(i,j)-gape
- e = _mm_max_epu8(e, h); // e=E'(i+1,j)
- _mm_store_si128(E + j, e); // save to E'(i+1,j)
- // now compute F'(i,j+1)
- f = _mm_subs_epu8(f, gape);
- f = _mm_max_epu8(f, h);
- // get H'(i-1,j) and prepare for the next j
- h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
- }
- // NB: we do not need to set E(i,j) as we disallow adjecent insertion and then deletion
- for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3; NB: H(i,j) updated in the lazy-F loop cannot exceed max
- f = _mm_slli_si128(f, 1);
- for (j = 0; LIKELY(j < slen); ++j) {
- h = _mm_load_si128(H1 + j);
- h = _mm_max_epu8(h, f); // h=H'(i,j)
- _mm_store_si128(H1 + j, h);
- h = _mm_subs_epu8(h, gapoe);
- f = _mm_subs_epu8(f, gape);
- cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero));
- if (UNLIKELY(cmp == 0xffff)) goto end_loop16;
- }
- }
-end_loop16:
- //int k;for (k=0;k<16;++k)printf("%d ", ((uint8_t*)&max)[k]);printf("\n");
- __max_16(imax, max); // imax is the maximum number in max
- if (imax >= minsc) { // write the b array; this condition adds branching unfornately
- if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) { // then append
- if (n_b == m_b) {
- m_b = m_b? m_b<<1 : 8;
- b = (uint64_t*)realloc(b, 8 * m_b);
- }
- b[n_b++] = (uint64_t)imax<<32 | i;
- } else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
- }
- if (imax > gmax) {
- gmax = imax; te = i; // te is the end position on the target
- for (j = 0; LIKELY(j < slen); ++j) // keep the H1 vector
- _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
- if (gmax + q->shift >= 255 || gmax >= endsc) break;
- }
- S = H1; H1 = H0; H0 = S; // swap H0 and H1
- }
- r.score = gmax + q->shift < 255? gmax : 255;
- r.te = te;
- if (r.score != 255) { // get a->qe, the end of query match; find the 2nd best score
- int max = -1, low, high, qlen = slen * 16;
- uint8_t *t = (uint8_t*)Hmax;
- for (i = 0; i < qlen; ++i, ++t)
- if ((int)*t > max) max = *t, r.qe = i / 16 + i % 16 * slen;
- //printf("%d,%d\n", max, gmax);
- if (b) {
- i = (r.score + q->max - 1) / q->max;
- low = te - i; high = te + i;
- for (i = 0; i < n_b; ++i) {
- int e = (int32_t)b[i];
- if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
- r.score2 = b[i]>>32, r.te2 = e;
- }
- }
- }
- free(b);
- return r;
-}
-
-kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra) // the first gap costs -(_o+_e)
-{
- int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
- uint64_t *b;
- __m128i zero, gapoe, gape, *H0, *H1, *E, *Hmax;
- kswr_t r;
-
-#define __max_8(ret, xx) do { \
- (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 8)); \
- (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 4)); \
- (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 2)); \
- (ret) = _mm_extract_epi16((xx), 0); \
- } while (0)
-
- // initialization
- r = g_defr;
- minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
- endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
- m_b = n_b = 0; b = 0;
- zero = _mm_set1_epi32(0);
- gapoe = _mm_set1_epi16(_gapo + _gape);
- gape = _mm_set1_epi16(_gape);
- H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
- slen = q->slen;
- for (i = 0; i < slen; ++i) {
- _mm_store_si128(E + i, zero);
- _mm_store_si128(H0 + i, zero);
- _mm_store_si128(Hmax + i, zero);
- }
- // the core loop
- for (i = 0; i < tlen; ++i) {
- int j, k, imax;
- __m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
- h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
- h = _mm_slli_si128(h, 2);
- for (j = 0; LIKELY(j < slen); ++j) {
- h = _mm_adds_epi16(h, *S++);
- e = _mm_load_si128(E + j);
- h = _mm_max_epi16(h, e);
- h = _mm_max_epi16(h, f);
- max = _mm_max_epi16(max, h);
- _mm_store_si128(H1 + j, h);
- h = _mm_subs_epu16(h, gapoe);
- e = _mm_subs_epu16(e, gape);
- e = _mm_max_epi16(e, h);
- _mm_store_si128(E + j, e);
- f = _mm_subs_epu16(f, gape);
- f = _mm_max_epi16(f, h);
- h = _mm_load_si128(H0 + j);
- }
- for (k = 0; LIKELY(k < 16); ++k) {
- f = _mm_slli_si128(f, 2);
- for (j = 0; LIKELY(j < slen); ++j) {
- h = _mm_load_si128(H1 + j);
- h = _mm_max_epi16(h, f);
- _mm_store_si128(H1 + j, h);
- h = _mm_subs_epu16(h, gapoe);
- f = _mm_subs_epu16(f, gape);
- if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
- }
- }
-end_loop8:
- __max_8(imax, max);
- if (imax >= minsc) {
- if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) {
- if (n_b == m_b) {
- m_b = m_b? m_b<<1 : 8;
- b = (uint64_t*)realloc(b, 8 * m_b);
- }
- b[n_b++] = (uint64_t)imax<<32 | i;
- } else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
- }
- if (imax > gmax) {
- gmax = imax; te = i;
- for (j = 0; LIKELY(j < slen); ++j)
- _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
- if (gmax >= endsc) break;
- }
- S = H1; H1 = H0; H0 = S;
- }
- r.score = gmax; r.te = te;
- {
- int max = -1, low, high, qlen = slen * 8;
- uint16_t *t = (uint16_t*)Hmax;
- for (i = 0, r.qe = -1; i < qlen; ++i, ++t)
- if ((int)*t > max) max = *t, r.qe = i / 8 + i % 8 * slen;
- if (b) {
- i = (r.score + q->max - 1) / q->max;
- low = te - i; high = te + i;
- for (i = 0; i < n_b; ++i) {
- int e = (int32_t)b[i];
- if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
- r.score2 = b[i]>>32, r.te2 = e;
- }
- }
- }
- free(b);
- return r;
-}
-
-static void revseq(int l, uint8_t *s)
-{
- int i, t;
- for (i = 0; i < l>>1; ++i)
- t = s[i], s[i] = s[l - 1 - i], s[l - 1 - i] = t;
-}
-
-kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry)
-{
- int size;
- kswq_t *q;
- kswr_t r, rr;
- kswr_t (*func)(kswq_t*, int, const uint8_t*, int, int, int);
-
- q = (qry && *qry)? *qry : ksw_qinit((xtra&KSW_XBYTE)? 1 : 2, qlen, query, m, mat);
- if (qry && *qry == 0) *qry = q;
- func = q->size == 2? ksw_i16 : ksw_u8;
- size = q->size;
- r = func(q, tlen, target, gapo, gape, xtra);
- if (qry == 0) free(q);
- if ((xtra&KSW_XSTART) == 0 || ((xtra&KSW_XSUBO) && r.score < (xtra&0xffff))) return r;
- revseq(r.qe + 1, query); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, not the position after the end
- q = ksw_qinit(size, r.qe + 1, query, m, mat);
- rr = func(q, tlen, target, gapo, gape, KSW_XSTOP | r.score);
- revseq(r.qe + 1, query); revseq(r.te + 1, target);
- free(q);
- if (r.score == rr.score)
- r.tb = r.te - rr.te, r.qb = r.qe - rr.qe;
- return r;
-}
-
-/********************
- *** SW extension ***
- ********************/
-
-typedef struct {
- int32_t h, e;
-} eh_t;
-
-int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *_qle, int *_tle)
-{
- eh_t *eh; // score array
- int8_t *qp; // query profile
- int i, j, k, gapoe = gapo + gape, beg, end, max, max_i, max_j, max_gap;
- if (h0 < 0) h0 = 0;
- // allocate memory
- qp = malloc(qlen * m);
- eh = calloc(qlen + 1, 8);
- // generate the query profile
- for (k = i = 0; k < m; ++k) {
- const int8_t *p = &mat[k * m];
- for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
- }
- // fill the first row
- eh[0].h = h0; eh[1].h = h0 > gapoe? h0 - gapoe : 0;
- for (j = 2; j <= qlen && eh[j-1].h > gape; ++j)
- eh[j].h = eh[j-1].h - gape;
- // adjust $w if it is too large
- k = m * m;
- for (i = 0, max = 0; i < k; ++i) // get the max score
- max = max > mat[i]? max : mat[i];
- max_gap = (int)((double)(qlen * max - gapo) / gape + 1.);
- max_gap = max_gap > 1? max_gap : 1;
- w = w < max_gap? w : max_gap;
- // DP loop
- max = h0, max_i = max_j = -1;
- beg = 0, end = qlen;
- for (i = 0; LIKELY(i < tlen); ++i) {
- int f = 0, h1, m = 0, mj = -1;
- int8_t *q = &qp[target[i] * qlen];
- // compute the first column
- h1 = h0 - (gapo + gape * (i + 1));
- if (h1 < 0) h1 = 0;
- // apply the band and the constraint (if provided)
- if (beg < i - w) beg = i - w;
- if (end > i + w + 1) end = i + w + 1;
- if (end > qlen) end = qlen;
- for (j = beg; LIKELY(j < end); ++j) {
- // At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
- // Similar to SSE2-SW, cells are computed in the following order:
- // H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
- // E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape
- // F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape
- eh_t *p = &eh[j];
- int h = p->h, e = p->e; // get H(i-1,j-1) and E(i-1,j)
- p->h = h1; // set H(i,j-1) for the next row
- h += q[j];
- h = h > e? h : e;
- h = h > f? h : f;
- h1 = h; // save H(i,j) to h1 for the next column
- mj = m > h? mj : j;
- m = m > h? m : h; // m is stored at eh[mj+1]
- h -= gapoe;
- h = h > 0? h : 0;
- e -= gape;
- e = e > h? e : h; // computed E(i+1,j)
- p->e = e; // save E(i+1,j) for the next row
- f -= gape;
- f = f > h? f : h; // computed F(i,j+1)
- }
- eh[end].h = h1; eh[end].e = 0;
- if (m == 0) break;
- if (m > max) max = m, max_i = i, max_j = mj;
- // update beg and end for the next round
- for (j = mj; j >= beg && eh[j].h; --j);
- beg = j + 1;
- for (j = mj + 2; j <= end && eh[j].h; ++j);
- end = j;
- //beg = 0; end = qlen; // uncomment this line for debugging
- }
- free(eh); free(qp);
- if (_qle) *_qle = max_j + 1;
- if (_tle) *_tle = max_i + 1;
- return max;
-}
-
-/********************
- * Global alignment *
- ********************/
-
-#define MINUS_INF -0x40000000
-
-static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len)
-{
- if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
- if (*n_cigar == *m_cigar) {
- *m_cigar = *m_cigar? (*m_cigar)<<1 : 4;
- cigar = realloc(cigar, (*m_cigar) << 2);
- }
- cigar[(*n_cigar)++] = len<<4 | op;
- } else cigar[(*n_cigar)-1] += len<<4;
- return cigar;
-}
-
-int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar_, uint32_t **cigar_)
-{
- eh_t *eh;
- int8_t *qp; // query profile
- int i, j, k, gapoe = gapo + gape, score, n_col;
- uint8_t *z; // backtrack matrix; in each cell: f<<4|e<<2|h; in principle, we can halve the memory, but backtrack will be a little more complex
- if (n_cigar_) *n_cigar_ = 0;
- // allocate memory
- n_col = qlen < 2*w+1? qlen : 2*w+1; // maximum #columns of the backtrack matrix
- z = malloc(n_col * tlen);
- qp = malloc(qlen * m);
- eh = calloc(qlen + 1, 8);
- // generate the query profile
- for (k = i = 0; k < m; ++k) {
- const int8_t *p = &mat[k * m];
- for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
- }
- // fill the first row
- eh[0].h = 0; eh[0].e = MINUS_INF;
- for (j = 1; j <= qlen && j <= w; ++j)
- eh[j].h = -(gapo + gape * j), eh[j].e = MINUS_INF;
- for (; j <= qlen; ++j) eh[j].h = eh[j].e = MINUS_INF; // everything is -inf outside the band
- // DP loop
- for (i = 0; LIKELY(i < tlen); ++i) { // target sequence is in the outer loop
- int32_t f = MINUS_INF, h1, beg, end;
- int8_t *q = &qp[target[i] * qlen];
- uint8_t *zi = &z[i * n_col];
- beg = i > w? i - w : 0;
- end = i + w + 1 < qlen? i + w + 1 : qlen; // only loop through [beg,end) of the query sequence
- h1 = beg == 0? -(gapo + gape * (i + 1)) : MINUS_INF;
- for (j = beg; LIKELY(j < end); ++j) {
- // This loop is organized in a similar way to ksw_extend() and ksw_sse2(), except:
- // 1) not checking h>0; 2) recording direction for backtracking
- eh_t *p = &eh[j];
- int32_t h = p->h, e = p->e;
- uint8_t d; // direction
- p->h = h1;
- h += q[j];
- d = h > e? 0 : 1;
- h = h > e? h : e;
- d = h > f? d : 2;
- h = h > f? h : f;
- h1 = h;
- h -= gapoe;
- e -= gape;
- d |= e > h? 1<<2 : 0;
- e = e > h? e : h;
- p->e = e;
- f -= gape;
- d |= f > h? 2<<4 : 0; // if we want to halve the memory, use one bit only, instead of two
- f = f > h? f : h;
- zi[j - beg] = d; // z[i,j] keeps h for the current cell and e/f for the next cell
- }
- eh[end].h = h1; eh[end].e = MINUS_INF;
- }
- score = eh[qlen].h;
- if (n_cigar_ && cigar_) { // backtrack
- int n_cigar = 0, m_cigar = 0, which = 0;
- uint32_t *cigar = 0, tmp;
- i = tlen - 1; k = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell
- while (i >= 0 && k >= 0) {
- which = z[i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;
- if (which == 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k;
- else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i;
- else cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k;
- }
- if (i >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);
- if (k >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1);
- for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
- tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
- *n_cigar_ = n_cigar, *cigar_ = cigar;
- }
- free(eh); free(qp); free(z);
- return score;
-}
-
-/*******************************************
- * Main function (not compiled by default) *
- *******************************************/
-
-#ifdef _KSW_MAIN
-
-#include <unistd.h>
-#include <stdio.h>
-#include <zlib.h>
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
-
-unsigned char seq_nt4_table[256] = {
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
-};
-
-int main(int argc, char *argv[])
-{
- int c, sa = 1, sb = 3, i, j, k, forward_only = 0, max_rseq = 0;
- int8_t mat[25];
- int gapo = 5, gape = 2, minsc = 0, xtra = KSW_XSTART;
- uint8_t *rseq = 0;
- gzFile fpt, fpq;
- kseq_t *kst, *ksq;
-
- // parse command line
- while ((c = getopt(argc, argv, "a:b:q:r:ft:1")) >= 0) {
- switch (c) {
- case 'a': sa = atoi(optarg); break;
- case 'b': sb = atoi(optarg); break;
- case 'q': gapo = atoi(optarg); break;
- case 'r': gape = atoi(optarg); break;
- case 't': minsc = atoi(optarg); break;
- case 'f': forward_only = 1; break;
- case '1': xtra |= KSW_XBYTE; break;
- }
- }
- if (optind + 2 > argc) {
- fprintf(stderr, "Usage: ksw [-1] [-f] [-a%d] [-b%d] [-q%d] [-r%d] [-t%d] <target.fa> <query.fa>\n", sa, sb, gapo, gape, minsc);
- return 1;
- }
- if (minsc > 0xffff) minsc = 0xffff;
- xtra |= KSW_XSUBO | minsc;
- // initialize scoring matrix
- for (i = k = 0; i < 4; ++i) {
- for (j = 0; j < 4; ++j)
- mat[k++] = i == j? sa : -sb;
- mat[k++] = 0; // ambiguous base
- }
- for (j = 0; j < 5; ++j) mat[k++] = 0;
- // open file
- fpt = gzopen(argv[optind], "r"); kst = kseq_init(fpt);
- fpq = gzopen(argv[optind+1], "r"); ksq = kseq_init(fpq);
- // all-pair alignment
- while (kseq_read(ksq) > 0) {
- kswq_t *q[2] = {0, 0};
- kswr_t r;
- for (i = 0; i < (int)ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]];
- if (!forward_only) { // reverse
- if ((int)ksq->seq.m > max_rseq) {
- max_rseq = ksq->seq.m;
- rseq = (uint8_t*)realloc(rseq, max_rseq);
- }
- for (i = 0, j = ksq->seq.l - 1; i < (int)ksq->seq.l; ++i, --j)
- rseq[j] = ksq->seq.s[i] == 4? 4 : 3 - ksq->seq.s[i];
- }
- gzrewind(fpt); kseq_rewind(kst);
- while (kseq_read(kst) > 0) {
- for (i = 0; i < (int)kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]];
- r = ksw_align(ksq->seq.l, (uint8_t*)ksq->seq.s, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[0]);
- if (r.score >= minsc)
- printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, r.qb, r.qe+1, r.score, r.score2, r.te2);
- if (rseq) {
- r = ksw_align(ksq->seq.l, rseq, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[1]);
- if (r.score >= minsc)
- printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, (int)ksq->seq.l - r.qb, (int)ksq->seq.l - 1 - r.qe, r.score, r.score2, r.te2);
- }
- }
- free(q[0]); free(q[1]);
- }
- free(rseq);
- kseq_destroy(kst); gzclose(fpt);
- kseq_destroy(ksq); gzclose(fpq);
- return 0;
-}
-#endif
diff --git a/debian/vendor-h2o/deps/klib/ksw.h b/debian/vendor-h2o/deps/klib/ksw.h
deleted file mode 100644
index 5162dc0..0000000
--- a/debian/vendor-h2o/deps/klib/ksw.h
+++ /dev/null
@@ -1,72 +0,0 @@
-#ifndef __AC_KSW_H
-#define __AC_KSW_H
-
-#include <stdint.h>
-
-#define KSW_XBYTE 0x10000
-#define KSW_XSTOP 0x20000
-#define KSW_XSUBO 0x40000
-#define KSW_XSTART 0x80000
-
-struct _kswq_t;
-typedef struct _kswq_t kswq_t;
-
-typedef struct {
- int score; // best score
- int te, qe; // target end and query end
- int score2, te2; // second best score and ending position on the target
- int tb, qb; // target start and query start
-} kswr_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- /**
- * Aligning two sequences
- *
- * @param qlen length of the query sequence (typically <tlen)
- * @param query query sequence with 0 <= query[i] < m
- * @param tlen length of the target sequence
- * @param target target sequence
- * @param m number of residue types
- * @param mat m*m scoring matrix in one-dimention array
- * @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)"
- * @param gape gap extension penalty
- * @param xtra extra information (see below)
- * @param qry query profile (see below)
- *
- * @return alignment information in a struct; unset values to -1
- *
- * When xtra==0, ksw_align() uses a signed two-byte integer to store a
- * score and only finds the best score and the end positions. The 2nd best
- * score or the start positions are not attempted. The default behavior can
- * be tuned by setting KSW_X* flags:
- *
- * KSW_XBYTE: use an unsigned byte to store a score. If overflow occurs,
- * kswr_t::score will be set to 255
- *
- * KSW_XSUBO: track the 2nd best score and the ending position on the
- * target if the 2nd best is higher than (xtra&0xffff)
- *
- * KSW_XSTOP: stop if the maximum score is above (xtra&0xffff)
- *
- * KSW_XSTART: find the start positions
- *
- * When *qry==NULL, ksw_align() will compute and allocate the query profile
- * and when the function returns, *qry will point to the profile, which can
- * be deallocated simply by free(). If one query is aligned against multiple
- * target sequences, *qry should be set to NULL during the first call and
- * freed after the last call. Note that qry can equal 0. In this case, the
- * query profile will be deallocated in ksw_align().
- */
- kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry);
-
- int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *_qle, int *_tle);
- int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *_n_cigar, uint32_t **_cigar);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kthread.c b/debian/vendor-h2o/deps/klib/kthread.c
deleted file mode 100644
index 80f84cb..0000000
--- a/debian/vendor-h2o/deps/klib/kthread.c
+++ /dev/null
@@ -1,143 +0,0 @@
-#include <pthread.h>
-#include <stdlib.h>
-#include <limits.h>
-
-/************
- * kt_for() *
- ************/
-
-struct kt_for_t;
-
-typedef struct {
- struct kt_for_t *t;
- long i;
-} ktf_worker_t;
-
-typedef struct kt_for_t {
- int n_threads;
- long n;
- ktf_worker_t *w;
- void (*func)(void*,long,int);
- void *data;
-} kt_for_t;
-
-static inline long steal_work(kt_for_t *t)
-{
- int i, min_i = -1;
- long k, min = LONG_MAX;
- for (i = 0; i < t->n_threads; ++i)
- if (min > t->w[i].i) min = t->w[i].i, min_i = i;
- k = __sync_fetch_and_add(&t->w[min_i].i, t->n_threads);
- return k >= t->n? -1 : k;
-}
-
-static void *ktf_worker(void *data)
-{
- ktf_worker_t *w = (ktf_worker_t*)data;
- long i;
- for (;;) {
- i = __sync_fetch_and_add(&w->i, w->t->n_threads);
- if (i >= w->t->n) break;
- w->t->func(w->t->data, i, w - w->t->w);
- }
- while ((i = steal_work(w->t)) >= 0)
- w->t->func(w->t->data, i, w - w->t->w);
- pthread_exit(0);
-}
-
-void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n)
-{
- int i;
- kt_for_t t;
- pthread_t *tid;
- t.func = func, t.data = data, t.n_threads = n_threads, t.n = n;
- t.w = (ktf_worker_t*)alloca(n_threads * sizeof(ktf_worker_t));
- tid = (pthread_t*)alloca(n_threads * sizeof(pthread_t));
- for (i = 0; i < n_threads; ++i)
- t.w[i].t = &t, t.w[i].i = i;
- for (i = 0; i < n_threads; ++i) pthread_create(&tid[i], 0, ktf_worker, &t.w[i]);
- for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
-}
-
-/*****************
- * kt_pipeline() *
- *****************/
-
-struct ktp_t;
-
-typedef struct {
- struct ktp_t *pl;
- int step, running;
- void *data;
-} ktp_worker_t;
-
-typedef struct ktp_t {
- void *shared;
- void *(*func)(void*, int, void*);
- int n_workers, n_steps;
- ktp_worker_t *workers;
- pthread_mutex_t mutex;
- pthread_cond_t cv;
-} ktp_t;
-
-static void *ktp_worker(void *data)
-{
- ktp_worker_t *w = (ktp_worker_t*)data;
- ktp_t *p = w->pl;
- while (w->step < p->n_steps) {
- // test whether we can kick off the job with this worker
- pthread_mutex_lock(&p->mutex);
- for (;;) {
- int i;
- // test whether another worker is doing the same step
- for (i = 0; i < p->n_workers; ++i) {
- if (w == &p->workers[i]) continue; // ignore itself
- if (p->workers[i].running && p->workers[i].step == w->step)
- break;
- }
- if (i == p->n_workers) break; // no other workers doing w->step; then this worker will
- pthread_cond_wait(&p->cv, &p->mutex);
- }
- w->running = 1;
- pthread_mutex_unlock(&p->mutex);
-
- // working on w->step
- w->data = p->func(p->shared, w->step, w->step? w->data : 0); // for the first step, input is NULL
-
- // update step and let other workers know
- pthread_mutex_lock(&p->mutex);
- w->step = w->step == p->n_steps - 1 || w->data? (w->step + 1) % p->n_steps : p->n_steps;
- w->running = 0;
- pthread_cond_broadcast(&p->cv);
- pthread_mutex_unlock(&p->mutex);
- }
- pthread_exit(0);
-}
-
-void kt_pipeline(int n_threads, void *(*func)(void*, int, void*), void *shared_data, int n_steps)
-{
- ktp_t aux;
- pthread_t *tid;
- int i;
-
- if (n_threads < 1) n_threads = 1;
- aux.n_workers = n_threads;
- aux.n_steps = n_steps;
- aux.func = func;
- aux.shared = shared_data;
- pthread_mutex_init(&aux.mutex, 0);
- pthread_cond_init(&aux.cv, 0);
-
- aux.workers = alloca(n_threads * sizeof(ktp_worker_t));
- for (i = 0; i < n_threads; ++i) {
- ktp_worker_t *w = &aux.workers[i];
- w->step = w->running = 0; w->pl = &aux; w->data = 0;
- }
-
- tid = alloca(n_threads * sizeof(pthread_t));
- for (i = 0; i < n_threads; ++i) pthread_create(&tid[i], 0, ktp_worker, &aux.workers[i]);
- for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
-
- pthread_mutex_destroy(&aux.mutex);
- pthread_cond_destroy(&aux.cv);
-}
diff --git a/debian/vendor-h2o/deps/klib/kurl.c b/debian/vendor-h2o/deps/klib/kurl.c
deleted file mode 100644
index 3bf9290..0000000
--- a/debian/vendor-h2o/deps/klib/kurl.c
+++ /dev/null
@@ -1,583 +0,0 @@
-#include <stdio.h>
-#include <fcntl.h>
-#include <ctype.h>
-#include <assert.h>
-#include <stdint.h>
-#include <stdlib.h>
-#include <unistd.h>
-#include <string.h>
-#include <curl/curl.h>
-#include "kurl.h"
-
-/**********************
- *** Core kurl APIs ***
- **********************/
-
-#define KU_DEF_BUFLEN 0x8000
-#define KU_MAX_SKIP (KU_DEF_BUFLEN<<1) // if seek step is smaller than this, skip
-
-#define kurl_isfile(u) ((u)->fd >= 0)
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-struct kurl_t {
- CURLM *multi; // cURL multi handler
- CURL *curl; // cURL easy handle
- uint8_t *buf; // buffer
- off_t off0; // offset of the first byte in the buffer; the actual file offset equals off0 + p_buf
- int fd; // file descriptor for a normal file; <0 for a remote file
- int m_buf; // max buffer size; for a remote file, CURL_MAX_WRITE_SIZE*2 is recommended
- int l_buf; // length of the buffer; l_buf == 0 iff the input read entirely; l_buf <= m_buf
- int p_buf; // file position in the buffer; p_buf <= l_buf
- int done_reading; // true if we can read nothing from the file; buffer may not be empty even if done_reading is set
- int err; // error code
- struct curl_slist *hdr;
-};
-
-typedef struct {
- char *url, *date, *auth;
-} s3aux_t;
-
-int kurl_init(void) // required for SSL and win32 socket; NOT thread safe
-{
- return curl_global_init(CURL_GLOBAL_DEFAULT);
-}
-
-void kurl_destroy(void)
-{
- curl_global_cleanup();
-}
-
-static int prepare(kurl_t *ku, int do_seek)
-{
- if (kurl_isfile(ku)) {
- if (do_seek && lseek(ku->fd, ku->off0, SEEK_SET) != ku->off0)
- return -1;
- } else { // FIXME: for S3, we need to re-authorize
- int rc;
- rc = curl_multi_remove_handle(ku->multi, ku->curl);
- rc = curl_easy_setopt(ku->curl, CURLOPT_RESUME_FROM, ku->off0);
- rc = curl_multi_add_handle(ku->multi, ku->curl);
- }
- ku->p_buf = ku->l_buf = 0; // empty the buffer
- return 0;
-}
-
-static size_t write_cb(char *ptr, size_t size, size_t nmemb, void *data) // callback required by cURL
-{
- kurl_t *ku = (kurl_t*)data;
- ssize_t nbytes = size * nmemb;
- if (nbytes + ku->l_buf > ku->m_buf)
- return CURL_WRITEFUNC_PAUSE;
- memcpy(ku->buf + ku->l_buf, ptr, nbytes);
- ku->l_buf += nbytes;
- return nbytes;
-}
-
-static int fill_buffer(kurl_t *ku) // fill the buffer
-{
- assert(ku->p_buf == ku->l_buf); // buffer is always used up when fill_buffer() is called; otherwise a bug
- ku->off0 += ku->l_buf;
- ku->p_buf = ku->l_buf = 0;
- if (ku->done_reading) return 0;
- if (kurl_isfile(ku)) {
- // The following block is equivalent to "ku->l_buf = read(ku->fd, ku->buf, ku->m_buf)" on Mac.
- // On Linux, the man page does not specify whether read() guarantees to read ku->m_buf bytes
- // even if ->fd references a normal file with sufficient remaining bytes.
- while (ku->l_buf < ku->m_buf) {
- int l;
- l = read(ku->fd, ku->buf + ku->l_buf, ku->m_buf - ku->l_buf);
- if (l == 0) break;
- ku->l_buf += l;
- }
- if (ku->l_buf < ku->m_buf) ku->done_reading = 1;
- } else {
- int n_running, rc;
- fd_set fdr, fdw, fde;
- do {
- int maxfd = -1;
- long curl_to = -1;
- struct timeval to;
- // the following is adaped from docs/examples/fopen.c
- to.tv_sec = 10, to.tv_usec = 0; // 10 seconds
- curl_multi_timeout(ku->multi, &curl_to);
- if (curl_to >= 0) {
- to.tv_sec = curl_to / 1000;
- if (to.tv_sec > 1) to.tv_sec = 1;
- else to.tv_usec = (curl_to % 1000) * 1000;
- }
- FD_ZERO(&fdr); FD_ZERO(&fdw); FD_ZERO(&fde);
- curl_multi_fdset(ku->multi, &fdr, &fdw, &fde, &maxfd); // FIXME: check return code
- if (maxfd >= 0 && (rc = select(maxfd+1, &fdr, &fdw, &fde, &to)) < 0) break;
- if (maxfd < 0) { // check curl_multi_fdset.3 about why we wait for 100ms here
- struct timespec req, rem;
- req.tv_sec = 0; req.tv_nsec = 100000000; // this is 100ms
- nanosleep(&req, &rem);
- }
- curl_easy_pause(ku->curl, CURLPAUSE_CONT);
- rc = curl_multi_perform(ku->multi, &n_running); // FIXME: check return code
- } while (n_running && ku->l_buf < ku->m_buf - CURL_MAX_WRITE_SIZE);
- if (ku->l_buf < ku->m_buf - CURL_MAX_WRITE_SIZE) ku->done_reading = 1;
- }
- return ku->l_buf;
-}
-
-int kurl_close(kurl_t *ku)
-{
- if (ku == 0) return 0;
- if (ku->fd < 0) {
- curl_multi_remove_handle(ku->multi, ku->curl);
- curl_easy_cleanup(ku->curl);
- curl_multi_cleanup(ku->multi);
- if (ku->hdr) curl_slist_free_all(ku->hdr);
- } else close(ku->fd);
- free(ku->buf);
- free(ku);
- return 0;
-}
-
-kurl_t *kurl_open(const char *url, kurl_opt_t *opt)
-{
- extern s3aux_t s3_parse(const char *url, const char *_id, const char *_secret, const char *fn);
- const char *p, *q;
- kurl_t *ku;
- int fd = -1, is_file = 1, failed = 0;
-
- p = strstr(url, "://");
- if (p && *p) {
- for (q = url; q != p; ++q)
- if (!isalnum(*q)) break;
- if (q == p) is_file = 0;
- }
- if (is_file && (fd = open(url, O_RDONLY)) < 0) return 0;
-
- ku = (kurl_t*)calloc(1, sizeof(kurl_t));
- ku->fd = is_file? fd : -1;
- if (!kurl_isfile(ku)) {
- ku->multi = curl_multi_init();
- ku->curl = curl_easy_init();
- if (strstr(url, "s3://") == url) {
- s3aux_t a;
- a = s3_parse(url, (opt? opt->s3keyid : 0), (opt? opt->s3secretkey : 0), (opt? opt->s3key_fn : 0));
- if (a.url == 0 || a.date == 0 || a.auth == 0) {
- kurl_close(ku);
- return 0;
- }
- ku->hdr = curl_slist_append(ku->hdr, a.date);
- ku->hdr = curl_slist_append(ku->hdr, a.auth);
- curl_easy_setopt(ku->curl, CURLOPT_URL, a.url);
- curl_easy_setopt(ku->curl, CURLOPT_HTTPHEADER, ku->hdr);
- free(a.date); free(a.auth); free(a.url);
- } else curl_easy_setopt(ku->curl, CURLOPT_URL, url);
- curl_easy_setopt(ku->curl, CURLOPT_WRITEDATA, ku);
- curl_easy_setopt(ku->curl, CURLOPT_VERBOSE, 0L);
- curl_easy_setopt(ku->curl, CURLOPT_NOSIGNAL, 1L);
- curl_easy_setopt(ku->curl, CURLOPT_WRITEFUNCTION, write_cb);
- curl_easy_setopt(ku->curl, CURLOPT_SSL_VERIFYPEER, 0L);
- curl_easy_setopt(ku->curl, CURLOPT_SSL_VERIFYHOST, 0L);
- curl_easy_setopt(ku->curl, CURLOPT_FOLLOWLOCATION, 1L);
- }
- ku->m_buf = KU_DEF_BUFLEN;
- if (!kurl_isfile(ku) && ku->m_buf < CURL_MAX_WRITE_SIZE * 2)
- ku->m_buf = CURL_MAX_WRITE_SIZE * 2; // for remote files, the buffer set to 2*CURL_MAX_WRITE_SIZE
- ku->buf = (uint8_t*)calloc(ku->m_buf, 1);
- if (kurl_isfile(ku)) failed = (fill_buffer(ku) <= 0);
- else failed = (prepare(ku, 0) < 0 || fill_buffer(ku) <= 0);
- if (failed) {
- kurl_close(ku);
- return 0;
- }
- return ku;
-}
-
-kurl_t *kurl_dopen(int fd)
-{
- kurl_t *ku;
- ku = (kurl_t*)calloc(1, sizeof(kurl_t));
- ku->fd = fd;
- ku->m_buf = KU_DEF_BUFLEN;
- ku->buf = (uint8_t*)calloc(ku->m_buf, 1);
- if (prepare(ku, 0) < 0 || fill_buffer(ku) <= 0) {
- kurl_close(ku);
- return 0;
- }
- return ku;
-}
-
-int kurl_buflen(kurl_t *ku, int len)
-{
- if (len <= 0 || len < ku->l_buf) return ku->m_buf;
- if (!kurl_isfile(ku) && len < CURL_MAX_WRITE_SIZE * 2) return ku->m_buf;
- ku->m_buf = len;
- kroundup32(ku->m_buf);
- ku->buf = (uint8_t*)realloc(ku->buf, ku->m_buf);
- return ku->m_buf;
-}
-
-ssize_t kurl_read(kurl_t *ku, void *buf, size_t nbytes)
-{
- ssize_t rest = nbytes;
- if (ku->l_buf == 0) return 0; // end-of-file
- while (rest) {
- if (ku->l_buf - ku->p_buf >= rest) {
- if (buf) memcpy((uint8_t*)buf + (nbytes - rest), ku->buf + ku->p_buf, rest);
- ku->p_buf += rest;
- rest = 0;
- } else {
- int ret;
- if (buf && ku->l_buf > ku->p_buf)
- memcpy((uint8_t*)buf + (nbytes - rest), ku->buf + ku->p_buf, ku->l_buf - ku->p_buf);
- rest -= ku->l_buf - ku->p_buf;
- ku->p_buf = ku->l_buf;
- ret = fill_buffer(ku);
- if (ret <= 0) break;
- }
- }
- return nbytes - rest;
-}
-
-off_t kurl_seek(kurl_t *ku, off_t offset, int whence) // FIXME: sometimes when seek() fails, read() will fail as well.
-{
- off_t new_off = -1, cur_off;
- int failed = 0, seek_end = 0;
- if (ku == 0) return -1;
- cur_off = ku->off0 + ku->p_buf;
- if (whence == SEEK_SET) new_off = offset;
- else if (whence == SEEK_CUR) new_off += cur_off + offset;
- else if (whence == SEEK_END && kurl_isfile(ku)) new_off = lseek(ku->fd, offset, SEEK_END), seek_end = 1;
- else { // not supported whence
- ku->err = KURL_INV_WHENCE;
- return -1;
- }
- if (new_off < 0) { // negtive absolute offset
- ku->err = KURL_SEEK_OUT;
- return -1;
- }
- if (!seek_end && new_off >= cur_off && new_off - cur_off + ku->p_buf < ku->l_buf) {
- ku->p_buf += new_off - cur_off;
- return ku->off0 + ku->p_buf;
- }
- if (seek_end || new_off < cur_off || new_off - cur_off > KU_MAX_SKIP) { // if jump is large, do actual seek
- ku->off0 = new_off;
- ku->done_reading = 0;
- if (prepare(ku, 1) < 0 || fill_buffer(ku) <= 0) failed = 1;
- } else { // if jump is small, read through
- off_t r;
- r = kurl_read(ku, 0, new_off - cur_off);
- if (r + cur_off != new_off) failed = 1; // out of range
- }
- if (failed) ku->err = KURL_SEEK_OUT, ku->l_buf = ku->p_buf = 0, new_off = -1;
- return new_off;
-}
-
-off_t kurl_tell(const kurl_t *ku)
-{
- if (ku == 0) return -1;
- return ku->off0 + ku->p_buf;
-}
-
-int kurl_eof(const kurl_t *ku)
-{
- if (ku == 0) return 1;
- return (ku->l_buf == 0); // unless file end, buffer should never be empty
-}
-
-int kurl_fileno(const kurl_t *ku)
-{
- if (ku == 0) return -1;
- return ku->fd;
-}
-
-int kurl_error(const kurl_t *ku)
-{
- if (ku == 0) return KURL_NULL;
- return ku->err;
-}
-
-/*****************
- *** HMAC-SHA1 ***
- *****************/
-
-/* This code is public-domain - it is based on libcrypt placed in the public domain by Wei Dai and other contributors. */
-
-#define HASH_LENGTH 20
-#define BLOCK_LENGTH 64
-
-typedef struct sha1nfo {
- union { uint8_t b[BLOCK_LENGTH]; uint32_t w[BLOCK_LENGTH/4]; } buf;
- uint8_t bufOffset;
- union { uint8_t b[HASH_LENGTH]; uint32_t w[HASH_LENGTH/4]; } state;
- uint32_t byteCount;
- uint8_t keyBuffer[BLOCK_LENGTH];
- uint8_t innerHash[HASH_LENGTH];
-} sha1nfo;
-
-void sha1_init(sha1nfo *s)
-{
- const uint8_t table[] = { 0x01,0x23,0x45,0x67, 0x89,0xab,0xcd,0xef, 0xfe,0xdc,0xba,0x98, 0x76,0x54,0x32,0x10, 0xf0,0xe1,0xd2,0xc3 };
- memcpy(s->state.b, table, HASH_LENGTH);
- s->byteCount = 0;
- s->bufOffset = 0;
-}
-
-#define rol32(value, bits) (((value) << (bits)) | ((value) >> (32 - (bits))))
-
-static void sha1_hashBlock(sha1nfo *s)
-{
- uint32_t i, t, a = s->state.w[0], b = s->state.w[1], c = s->state.w[2], d = s->state.w[3], e = s->state.w[4];
- for (i = 0; i < 80; i++) {
- if (i >= 16) {
- t = s->buf.w[(i+13)&15] ^ s->buf.w[(i+8)&15] ^ s->buf.w[(i+2)&15] ^ s->buf.w[i&15];
- s->buf.w[i&15] = rol32(t, 1);
- }
- if (i < 20) t = 0x5a827999 + (d ^ (b & (c ^ d)));
- else if (i < 40) t = 0x6ed9eba1 + (b ^ c ^ d);
- else if (i < 60) t = 0x8f1bbcdc + ((b & c) | (d & (b | c)));
- else t = 0xca62c1d6 + (b ^ c ^ d);
- t += rol32(a, 5) + e + s->buf.w[i&15];
- e = d; d = c; c = rol32(b, 30); b = a; a = t;
- }
- s->state.w[0] += a; s->state.w[1] += b; s->state.w[2] += c; s->state.w[3] += d; s->state.w[4] += e;
-}
-
-static inline void sha1_add(sha1nfo *s, uint8_t data)
-{
- s->buf.b[s->bufOffset ^ 3] = data;
- if (++s->bufOffset == BLOCK_LENGTH) {
- sha1_hashBlock(s);
- s->bufOffset = 0;
- }
-}
-
-void sha1_write1(sha1nfo *s, uint8_t data)
-{
- ++s->byteCount;
- sha1_add(s, data);
-}
-
-void sha1_write(sha1nfo *s, const char *data, size_t len)
-{
- while (len--) sha1_write1(s, (uint8_t)*data++);
-}
-
-const uint8_t *sha1_final(sha1nfo *s)
-{
- int i;
- sha1_add(s, 0x80);
- while (s->bufOffset != 56) sha1_add(s, 0);
- sha1_add(s, 0);
- sha1_add(s, 0);
- sha1_add(s, 0);
- sha1_add(s, s->byteCount >> 29);
- sha1_add(s, s->byteCount >> 21);
- sha1_add(s, s->byteCount >> 13);
- sha1_add(s, s->byteCount >> 5);
- sha1_add(s, s->byteCount << 3);
- for (i = 0; i < 5; ++i) {
- uint32_t a = s->state.w[i];
- s->state.w[i] = a<<24 | (a<<8&0x00ff0000) | (a>>8&0x0000ff00) | a>>24;
- }
- return s->state.b;
-}
-
-#define HMAC_IPAD 0x36
-#define HMAC_OPAD 0x5c
-
-void sha1_init_hmac(sha1nfo *s, const uint8_t* key, int l_key)
-{
- uint8_t i;
- memset(s->keyBuffer, 0, BLOCK_LENGTH);
- if (l_key > BLOCK_LENGTH) {
- sha1_init(s);
- while (l_key--) sha1_write1(s, *key++);
- memcpy(s->keyBuffer, sha1_final(s), HASH_LENGTH);
- } else memcpy(s->keyBuffer, key, l_key);
- sha1_init(s);
- for (i = 0; i < BLOCK_LENGTH; ++i)
- sha1_write1(s, s->keyBuffer[i] ^ HMAC_IPAD);
-}
-
-const uint8_t *sha1_final_hmac(sha1nfo *s)
-{
- uint8_t i;
- memcpy(s->innerHash, sha1_final(s), HASH_LENGTH);
- sha1_init(s);
- for (i = 0; i < BLOCK_LENGTH; ++i) sha1_write1(s, s->keyBuffer[i] ^ HMAC_OPAD);
- for (i = 0; i < HASH_LENGTH; ++i) sha1_write1(s, s->innerHash[i]);
- return sha1_final(s);
-}
-
-/*******************
- *** S3 protocol ***
- *******************/
-
-#include <time.h>
-#include <ctype.h>
-
-static void s3_sign(const char *key, const char *data, char out[29])
-{
- const char *b64tab = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
- const uint8_t *digest;
- int i, j, rest;
- sha1nfo s;
- sha1_init_hmac(&s, (uint8_t*)key, strlen(key));
- sha1_write(&s, data, strlen(data));
- digest = sha1_final_hmac(&s);
- for (j = i = 0, rest = 8; i < 20; ++j) { // base64 encoding
- if (rest <= 6) {
- int next = i < 19? digest[i+1] : 0;
- out[j] = b64tab[(int)(digest[i] << (6-rest) & 0x3f) | next >> (rest+2)], ++i, rest += 2;
- } else out[j] = b64tab[(int)digest[i] >> (rest-6) & 0x3f], rest -= 6;
- }
- out[j++] = '='; out[j] = 0; // SHA1 digest always has 160 bits, or 20 bytes. We need one '=' at the end.
-}
-
-static char *s3_read_awssecret(const char *fn)
-{
- char *p, *secret, buf[128], *path;
- FILE *fp;
- int l;
- if (fn == 0) {
- char *home;
- home = getenv("HOME");
- if (home == 0) return 0;
- l = strlen(home) + 12;
- path = (char*)malloc(strlen(home) + 12);
- strcat(strcpy(path, home), "/.awssecret");
- } else path = (char*)fn;
- fp = fopen(path, "r");
- if (path != fn) free(path);
- if (fp == 0) return 0;
- l = fread(buf, 1, 127, fp);
- fclose(fp);
- buf[l] = 0;
- for (p = buf; *p != 0 && *p != '\n'; ++p);
- if (*p == 0) return 0;
- *p = 0; secret = p + 1;
- for (++p; *p != 0 && *p != '\n'; ++p);
- *p = 0;
- l = p - buf + 1;
- p = (char*)malloc(l);
- memcpy(p, buf, l);
- return p;
-}
-
-typedef struct { int l, m; char *s; } kstring_t;
-
-static inline int kputsn(const char *p, int l, kstring_t *s)
-{
- if (s->l + l + 1 >= s->m) {
- s->m = s->l + l + 2;
- kroundup32(s->m);
- s->s = (char*)realloc(s->s, s->m);
- }
- memcpy(s->s + s->l, p, l);
- s->l += l;
- s->s[s->l] = 0;
- return l;
-}
-
-s3aux_t s3_parse(const char *url, const char *_id, const char *_secret, const char *fn_secret)
-{
- const char *id, *secret, *bucket, *obj;
- char *id_secret = 0, date[64], sig[29];
- time_t t;
- struct tm tmt;
- s3aux_t a = {0,0};
- kstring_t str = {0,0,0};
- // parse URL
- if (strstr(url, "s3://") != url) return a;
- bucket = url + 5;
- for (obj = bucket; *obj && *obj != '/'; ++obj);
- if (*obj == 0) return a; // no object
- // acquire AWS credential and time
- if (_id == 0 || _secret == 0) {
- id_secret = s3_read_awssecret(fn_secret);
- if (id_secret == 0) return a; // fail to read the AWS credential
- id = id_secret;
- secret = id_secret + strlen(id) + 1;
- } else id = _id, secret = _secret;
- // compose URL for curl
- kputsn("https://", 8, &str);
- kputsn(bucket, obj - bucket, &str);
- kputsn(".s3.amazonaws.com", 17, &str);
- kputsn(obj, strlen(obj), &str);
- a.url = str.s;
- // compose the Date line
- str.l = str.m = 0; str.s = 0;
- t = time(0);
- strftime(date, 64, "%a, %d %b %Y %H:%M:%S +0000", gmtime_r(&t, &tmt));
- kputsn("Date: ", 6, &str);
- kputsn(date, strlen(date), &str);
- a.date = str.s;
- // compose the string to sign and sign it
- str.l = str.m = 0; str.s = 0;
- kputsn("GET\n\n\n", 6, &str);
- kputsn(date, strlen(date), &str);
- kputsn("\n", 1, &str);
- kputsn(bucket-1, strlen(bucket-1), &str);
- s3_sign(secret, str.s, sig);
- // compose the Authorization line
- str.l = 0;
- kputsn("Authorization: AWS ", 19, &str);
- kputsn(id, strlen(id), &str);
- kputsn(":", 1, &str);
- kputsn(sig, strlen(sig), &str);
- a.auth = str.s;
-// printf("curl -H '%s' -H '%s' %s\n", a.date, a.auth, a.url);
- return a;
-}
-
-/*********************
- *** Main function ***
- *********************/
-
-#ifdef KURL_MAIN
-int main(int argc, char *argv[])
-{
- kurl_t *f;
- int c, l, l_buf = 0x10000;
- off_t start = 0, rest = -1;
- uint8_t *buf;
- char *p;
- kurl_opt_t opt;
-
- memset(&opt, 0, sizeof(kurl_opt_t));
- while ((c = getopt(argc, argv, "c:l:a:")) >= 0) {
- if (c == 'c') start = strtol(optarg, &p, 0);
- else if (c == 'l') rest = strtol(optarg, &p, 0);
- else if (c == 'a') opt.s3key_fn = optarg;
- }
- if (optind == argc) {
- fprintf(stderr, "Usage: kurl [-c start] [-l length] <url>\n");
- return 1;
- }
- kurl_init();
- f = kurl_open(argv[optind], &opt);
- if (f == 0) {
- fprintf(stderr, "ERROR: fail to open URL\n");
- return 2;
- }
- if (start > 0) {
- if (kurl_seek(f, start, SEEK_SET) < 0) {
- kurl_close(f);
- fprintf(stderr, "ERROR: fail to seek\n");
- return 3;
- }
- }
- buf = (uint8_t*)calloc(l_buf, 1);
- while (rest != 0) {
- int to_read = rest > 0 && rest < l_buf? rest : l_buf;
- l = kurl_read(f, buf, to_read);
- if (l == 0) break;
- fwrite(buf, 1, l, stdout);
- rest -= l;
- }
- free(buf);
- kurl_close(f);
- kurl_destroy();
- return 0;
-}
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kurl.h b/debian/vendor-h2o/deps/klib/kurl.h
deleted file mode 100644
index f07f641..0000000
--- a/debian/vendor-h2o/deps/klib/kurl.h
+++ /dev/null
@@ -1,57 +0,0 @@
-#ifndef KURL_H
-#define KURL_H
-
-#include <sys/types.h>
-
-#define KURL_NULL 1
-#define KURL_INV_WHENCE 2
-#define KURL_SEEK_OUT 3
-#define KURL_NO_AUTH 4
-
-struct kurl_t;
-typedef struct kurl_t kurl_t;
-
-typedef struct {
- const char *s3keyid;
- const char *s3secretkey;
- const char *s3key_fn;
-} kurl_opt_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-int kurl_init(void);
-void kurl_destroy(void);
-
-kurl_t *kurl_open(const char *url, kurl_opt_t *opt);
-kurl_t *kurl_dopen(int fd);
-int kurl_close(kurl_t *ku);
-ssize_t kurl_read(kurl_t *ku, void *buf, size_t nbytes);
-off_t kurl_seek(kurl_t *ku, off_t offset, int whence);
-int kurl_buflen(kurl_t *ku, int len);
-
-off_t kurl_tell(const kurl_t *ku);
-int kurl_eof(const kurl_t *ku);
-int kurl_fileno(const kurl_t *ku);
-int kurl_error(const kurl_t *ku);
-
-#ifdef __cplusplus
-}
-#endif
-
-#ifndef KNETFILE_H
-#define KNETFILE_H
-typedef kurl_t knetFile;
-#define knet_open(fn, mode) kurl_open(fn, 0)
-#define knet_dopen(fd, mode) kurl_dopen(fd)
-#define knet_close(fp) kurl_close(fp)
-#define knet_read(fp, buf, len) kurl_read(fp, buf, len)
-#define knet_seek(fp, off, whence) kurl_seek(fp, off, whence)
-#define knet_tell(fp) kurl_tell(fp)
-#define knet_fileno(fp) kurl_fileno(fp)
-#define knet_win32_init() kurl_init()
-#define knet_win32_destroy() kurl_destroy()
-#endif
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/kvec.h b/debian/vendor-h2o/deps/klib/kvec.h
deleted file mode 100644
index 676be8b..0000000
--- a/debian/vendor-h2o/deps/klib/kvec.h
+++ /dev/null
@@ -1,90 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008, by Attractive Chaos <attractor@live.co.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.
-*/
-
-/*
- An example:
-
-#include "kvec.h"
-int main() {
- kvec_t(int) array;
- kv_init(array);
- kv_push(int, array, 10); // append
- kv_a(int, array, 20) = 5; // dynamic
- kv_A(array, 20) = 4; // static
- kv_destroy(array);
- return 0;
-}
-*/
-
-/*
- 2008-09-22 (0.1.0):
-
- * The initial version.
-
-*/
-
-#ifndef AC_KVEC_H
-#define AC_KVEC_H
-
-#include <stdlib.h>
-
-#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-
-#define kvec_t(type) struct { size_t n, m; type *a; }
-#define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
-#define kv_destroy(v) free((v).a)
-#define kv_A(v, i) ((v).a[(i)])
-#define kv_pop(v) ((v).a[--(v).n])
-#define kv_size(v) ((v).n)
-#define kv_max(v) ((v).m)
-
-#define kv_resize(type, v, s) ((v).m = (s), (v).a = (type*)realloc((v).a, sizeof(type) * (v).m))
-
-#define kv_copy(type, v1, v0) do { \
- if ((v1).m < (v0).n) kv_resize(type, v1, (v0).n); \
- (v1).n = (v0).n; \
- memcpy((v1).a, (v0).a, sizeof(type) * (v0).n); \
- } while (0) \
-
-#define kv_push(type, v, x) do { \
- if ((v).n == (v).m) { \
- (v).m = (v).m? (v).m<<1 : 2; \
- (v).a = (type*)realloc((v).a, sizeof(type) * (v).m); \
- } \
- (v).a[(v).n++] = (x); \
- } while (0)
-
-#define kv_pushp(type, v) (((v).n == (v).m)? \
- ((v).m = ((v).m? (v).m<<1 : 2), \
- (v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
- : 0), ((v).a + ((v).n++))
-
-#define kv_a(type, v, i) (((v).m <= (size_t)(i)? \
- ((v).m = (v).n = (i) + 1, kv_roundup32((v).m), \
- (v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
- : (v).n <= (size_t)(i)? (v).n = (i) + 1 \
- : 0), (v).a[(i)])
-
-#endif
diff --git a/debian/vendor-h2o/deps/klib/lua/bio.lua b/debian/vendor-h2o/deps/klib/lua/bio.lua
deleted file mode 100644
index c9f2200..0000000
--- a/debian/vendor-h2o/deps/klib/lua/bio.lua
+++ /dev/null
@@ -1,149 +0,0 @@
--- bioinformatics routines
-
--- Description: read a fasta/fastq file
-local function readseq(fp)
- local finished, last = false, nil;
- return function()
- local match;
- if finished then return nil end
- if (last == nil) then -- the first record or a record following a fastq
- for l in fp:lines() do
- if l:byte(1) == 62 or l:byte(1) == 64 then -- ">" || "@"
- last = l;
- break;
- end
- end
- if last == nil then
- finished = true;
- return nil;
- end
- end
- local tmp = last:find("%s");
- name = (tmp and last:sub(2, tmp-1)) or last:sub(2); -- sequence name
- local seqs = {};
- local c; -- the first character of the last line
- last = nil;
- for l in fp:lines() do -- read sequence
- c = l:byte(1);
- if c == 62 or c == 64 or c == 43 then
- last = l;
- break;
- end
- table.insert(seqs, l);
- end
- if last == nil then finished = true end -- end of file
- if c ~= 43 then return name, table.concat(seqs) end -- a fasta record
- local seq, len = table.concat(seqs), 0; -- prepare to parse quality
- seqs = {};
- for l in fp:lines() do -- read quality
- table.insert(seqs, l);
- len = len + #l;
- if len >= #seq then
- last = nil;
- return name, seq, table.concat(seqs);
- end
- end
- finished = true;
- return name, seq;
- end
-end
-
--- extract subsequence from a fasta file indexe by samtools faidx
-local function faidxsub(fn)
- local fpidx = io.open(fn .. ".fai");
- if fpidx == nil then
- io.stderr:write("[faidxsub] fail to open the FASTA index file.\n");
- return nil
- end
- local idx = {};
- for l in fpidx:lines() do
- local name, len, offset, line_blen, line_len = l:match("(%S+)%s(%d+)%s(%d+)%s(%d+)%s(%d+)");
- if name then
- idx[name] = {tonumber(len), offset, line_blen, line_len};
- end
- end
- fpidx:close();
- local fp = io.open(fn);
- return function(name, beg_, end_) -- 0-based coordinate
- if name == nil then fp:close(); return nil; end
- if idx[name] then
- local a = idx[name];
- beg_ = beg_ or 0;
- end_ = end_ or a[1];
- end_ = (end_ <= a[1] and end_) or a[1];
- local fb, fe = math.floor(beg_ / a[3]), math.floor(end_ / a[3]);
- local qb, qe = beg_ - fb * a[3], end_ - fe * a[3];
- fp:seek("set", a[2] + fb * a[4] + qb);
- local s = fp:read((fe - fb) * a[4] + (qe - qb)):gsub("%s", "");
- return s;
- end
- end
-end
-
---Description: Index a list of intervals and test if a given interval overlaps with the list
---Example: lua -lbio -e 'a={{100,201},{200,300},{400,600}};f=bio.intvovlp(a);print(f(600,700))'
---[[
- By default, we keep for each tiling 8192 window the interval overlaping the
- window while having the smallest start position. This method may not work
- well when most intervals are small but few intervals span a long distance.
-]]--
-local function intvovlp(intv, bits)
- bits = bits or 13 -- the default bin size is 8192 = 1<<13
- table.sort(intv, function(a,b) return a[1] < b[1] end) -- sort by the start
- -- merge intervals; the step speeds up testing, but can be skipped
- local b, e, k = -1, -1, 1
- for i = 1, #intv do
- if e < intv[i][1] then
- if e >= 0 then intv[k], k = {b, e}, k + 1 end
- b, e = intv[i][1], intv[i][2]
- else e = intv[i][2] end
- end
- if e >= 0 then intv[k] = {b, e} end
- while #a > k do table.remove(a) end -- truncate the interval list
- -- build the index for the list of intervals
- local idx, size, max = {}, math.pow(2, bits), 0
- for i = 1, #a do
- b = math.modf(intv[i][1] / size)
- e = math.modf(intv[i][2] / size)
- if b == e then idx[b] = idx[b] or i
- else for j = b, e do idx[j] = idx[j] or i end end
- max = (max > e and max) or e
- end
- -- return a function (closure)
- return function(_beg, _end)
- local x = math.modf(_beg / size)
- if x > max then return false end
- local off = idx[x]; -- the start bin
- if off == nil then -- the following is not the best in efficiency
- for i = x - 1, 0, -1 do -- find the minimum bin with a value
- if idx[i] ~= nil then off = idx[i]; break; end
- end
- if off == nil then return false end
- end
- for i = off, #intv do -- start from off and search for overlaps
- if intv[i][1] >= _end then return false
- elseif intv[i][2] > _beg then return true end
- end
- return false
- end
-end
-
-bio = {
- readseq = readseq,
- faidxsub = faidxsub,
- intvovlp = intvovlp
-}
-
-bio.nt16 = {
-[0]=15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, 15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15,
- 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, 15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
-}
-bio.ntcnt = { [0]=4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 }
-bio.ntcomp = { [0]=0, 8, 4, 12, 2, 10, 9, 14, 1, 6, 5, 13, 3, 11, 7, 15 }
-bio.ntrev = 'XACMGRSVTWYHKDBN'
diff --git a/debian/vendor-h2o/deps/klib/lua/klib.lua b/debian/vendor-h2o/deps/klib/lua/klib.lua
deleted file mode 100644
index bfe52f7..0000000
--- a/debian/vendor-h2o/deps/klib/lua/klib.lua
+++ /dev/null
@@ -1,677 +0,0 @@
---[[
- The MIT License
-
- Copyright (c) 2011, Attractive Chaos <attractor@live.co.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.
-]]--
-
---[[
- This is a Lua library, more exactly a collection of Lua snippets, covering
- utilities (e.g. getopt), string operations (e.g. split), statistics (e.g.
- Fisher's exact test), special functions (e.g. logarithm gamma) and matrix
- operations (e.g. Gauss-Jordan elimination). The routines are designed to be
- as independent as possible, such that one can copy-paste relevant pieces of
- code without worrying about additional library dependencies.
-
- If you use routines from this library, please include the licensing
- information above where appropriate.
-]]--
-
---[[
- Library functions and dependencies. "a>b" means "a is required by b"; "b<a"
- means "b depends on a".
-
- os.getopt()
- string:split()
- io.xopen()
- table.ksmall()
- table.shuffle()
- math.lgamma() >math.lbinom() >math.igamma()
- math.igamma() <math.lgamma() >matrix.chi2()
- math.erfc()
- math.lbinom() <math.lgamma() >math.fisher_exact()
- math.bernstein_poly() <math.lbinom()
- math.fisher_exact() <math.lbinom()
- math.jackknife()
- math.pearson()
- math.spearman()
- math.fmin()
- matrix
- matrix.add()
- matrix.T() >matrix.mul()
- matrix.mul() <matrix.T()
- matrix.tostring()
- matrix.chi2() <math.igamma()
- matrix.solve()
-]]--
-
--- Description: getopt() translated from the BSD getopt(); compatible with the default Unix getopt()
---[[ Example:
- for o, a in os.getopt(arg, 'a:b') do
- print(o, a)
- end
-]]--
-function os.getopt(args, ostr)
- local arg, place = nil, 0;
- return function ()
- if place == 0 then -- update scanning pointer
- place = 1
- if #args == 0 or args[1]:sub(1, 1) ~= '-' then place = 0; return nil end
- if #args[1] >= 2 then
- place = place + 1
- if args[1]:sub(2, 2) == '-' then -- found "--"
- place = 0
- table.remove(args, 1);
- return nil;
- end
- end
- end
- local optopt = args[1]:sub(place, place);
- place = place + 1;
- local oli = ostr:find(optopt);
- if optopt == ':' or oli == nil then -- unknown option
- if optopt == '-' then return nil end
- if place > #args[1] then
- table.remove(args, 1);
- place = 0;
- end
- return '?';
- end
- oli = oli + 1;
- if ostr:sub(oli, oli) ~= ':' then -- do not need argument
- arg = nil;
- if place > #args[1] then
- table.remove(args, 1);
- place = 0;
- end
- else -- need an argument
- if place <= #args[1] then -- no white space
- arg = args[1]:sub(place);
- else
- table.remove(args, 1);
- if #args == 0 then -- an option requiring argument is the last one
- place = 0;
- if ostr:sub(1, 1) == ':' then return ':' end
- return '?';
- else arg = args[1] end
- end
- table.remove(args, 1);
- place = 0;
- end
- return optopt, arg;
- end
-end
-
--- Description: string split
-function string:split(sep, n)
- local a, start = {}, 1;
- sep = sep or "%s+";
- repeat
- local b, e = self:find(sep, start);
- if b == nil then
- table.insert(a, self:sub(start));
- break
- end
- a[#a+1] = self:sub(start, b - 1);
- start = e + 1;
- if n and #a == n then
- table.insert(a, self:sub(start));
- break
- end
- until start > #self;
- return a;
-end
-
--- Description: smart file open
-function io.xopen(fn, mode)
- mode = mode or 'r';
- if fn == nil then return io.stdin;
- elseif fn == '-' then return (mode == 'r' and io.stdin) or io.stdout;
- elseif fn:sub(-3) == '.gz' then return (mode == 'r' and io.popen('gzip -dc ' .. fn, 'r')) or io.popen('gzip > ' .. fn, 'w');
- elseif fn:sub(-4) == '.bz2' then return (mode == 'r' and io.popen('bzip2 -dc ' .. fn, 'r')) or io.popen('bgzip2 > ' .. fn, 'w');
- else return io.open(fn, mode) end
-end
-
--- Description: find the k-th smallest element in an array (Ref. http://ndevilla.free.fr/median/)
-function table.ksmall(arr, k)
- local low, high = 1, #arr;
- while true do
- if high <= low then return arr[k] end
- if high == low + 1 then
- if arr[high] < arr[low] then arr[high], arr[low] = arr[low], arr[high] end;
- return arr[k];
- end
- local mid = math.floor((high + low) / 2);
- if arr[high] < arr[mid] then arr[mid], arr[high] = arr[high], arr[mid] end
- if arr[high] < arr[low] then arr[low], arr[high] = arr[high], arr[low] end
- if arr[low] < arr[mid] then arr[low], arr[mid] = arr[mid], arr[low] end
- arr[mid], arr[low+1] = arr[low+1], arr[mid];
- local ll, hh = low + 1, high;
- while true do
- repeat ll = ll + 1 until arr[ll] >= arr[low]
- repeat hh = hh - 1 until arr[low] >= arr[hh]
- if hh < ll then break end
- arr[ll], arr[hh] = arr[hh], arr[ll];
- end
- arr[low], arr[hh] = arr[hh], arr[low];
- if hh <= k then low = ll end
- if hh >= k then high = hh - 1 end
- end
-end
-
--- Description: shuffle/permutate an array
-function table.shuffle(a)
- for i = #a, 1, -1 do
- local j = math.random(i)
- a[j], a[i] = a[i], a[j]
- end
-end
-
---
--- Mathematics
---
-
--- Description: log gamma function
--- Required by: math.lbinom()
--- Reference: AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245
-function math.lgamma(z)
- local x;
- x = 0.1659470187408462e-06 / (z+7);
- x = x + 0.9934937113930748e-05 / (z+6);
- x = x - 0.1385710331296526 / (z+5);
- x = x + 12.50734324009056 / (z+4);
- x = x - 176.6150291498386 / (z+3);
- x = x + 771.3234287757674 / (z+2);
- x = x - 1259.139216722289 / (z+1);
- x = x + 676.5203681218835 / z;
- x = x + 0.9999999999995183;
- return math.log(x) - 5.58106146679532777 - z + (z-0.5) * math.log(z+6.5);
-end
-
--- Description: regularized incomplete gamma function
--- Dependent on: math.lgamma()
---[[
- Formulas are taken from Wiki, with additional input from Numerical
- Recipes in C (for modified Lentz's algorithm) and AS245
- (http://lib.stat.cmu.edu/apstat/245).
-
- A good online calculator is available at:
-
- http://www.danielsoper.com/statcalc/calc23.aspx
-
- It calculates upper incomplete gamma function, which equals
- math.igamma(s,z,true)*math.exp(math.lgamma(s))
-]]--
-function math.igamma(s, z, complement)
-
- local function _kf_gammap(s, z)
- local sum, x = 1, 1;
- for k = 1, 100 do
- x = x * z / (s + k);
- sum = sum + x;
- if x / sum < 1e-14 then break end
- end
- return math.exp(s * math.log(z) - z - math.lgamma(s + 1.) + math.log(sum));
- end
-
- local function _kf_gammaq(s, z)
- local C, D, f, TINY;
- f = 1. + z - s; C = f; D = 0.; TINY = 1e-290;
- -- Modified Lentz's algorithm for computing continued fraction. See Numerical Recipes in C, 2nd edition, section 5.2
- for j = 1, 100 do
- local d;
- local a, b = j * (s - j), j*2 + 1 + z - s;
- D = b + a * D;
- if D < TINY then D = TINY end
- C = b + a / C;
- if C < TINY then C = TINY end
- D = 1. / D;
- d = C * D;
- f = f * d;
- if math.abs(d - 1) < 1e-14 then break end
- end
- return math.exp(s * math.log(z) - z - math.lgamma(s) - math.log(f));
- end
-
- if complement then
- return ((z <= 1 or z < s) and 1 - _kf_gammap(s, z)) or _kf_gammaq(s, z);
- else
- return ((z <= 1 or z < s) and _kf_gammap(s, z)) or (1 - _kf_gammaq(s, z));
- end
-end
-
-math.M_SQRT2 = 1.41421356237309504880 -- sqrt(2)
-math.M_SQRT1_2 = 0.70710678118654752440 -- 1/sqrt(2)
-
--- Description: complement error function erfc(x): \Phi(x) = 0.5 * erfc(-x/M_SQRT2)
-function math.erfc(x)
- local z = math.abs(x) * math.M_SQRT2
- if z > 37 then return (x > 0 and 0) or 2 end
- local expntl = math.exp(-0.5 * z * z)
- local p
- if z < 10. / math.M_SQRT2 then -- for small z
- p = expntl * ((((((.03526249659989109 * z + .7003830644436881) * z + 6.37396220353165) * z + 33.912866078383)
- * z + 112.0792914978709) * z + 221.2135961699311) * z + 220.2068679123761)
- / (((((((.08838834764831844 * z + 1.755667163182642) * z + 16.06417757920695) * z + 86.78073220294608)
- * z + 296.5642487796737) * z + 637.3336333788311) * z + 793.8265125199484) * z + 440.4137358247522);
- else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65))))) end
- return (x > 0 and 2 * p) or 2 * (1 - p)
-end
-
--- Description: log binomial coefficient
--- Dependent on: math.lgamma()
--- Required by: math.fisher_exact()
-function math.lbinom(n, m)
- if m == nil then
- local a = {};
- a[0], a[n] = 0, 0;
- local t = math.lgamma(n+1);
- for m = 1, n-1 do a[m] = t - math.lgamma(m+1) - math.lgamma(n-m+1) end
- return a;
- else return math.lgamma(n+1) - math.lgamma(m+1) - math.lgamma(n-m+1) end
-end
-
--- Description: Berstein polynomials (mainly for Bezier curves)
--- Dependent on: math.lbinom()
--- Note: to compute derivative: let beta_new[i]=beta[i+1]-beta[i]
-function math.bernstein_poly(beta)
- local n = #beta - 1;
- local lbc = math.lbinom(n); -- log binomial coefficients
- return function (t)
- assert(t >= 0 and t <= 1);
- if t == 0 then return beta[1] end
- if t == 1 then return beta[n+1] end
- local sum, logt, logt1 = 0, math.log(t), math.log(1-t);
- for i = 0, n do sum = sum + beta[i+1] * math.exp(lbc[i] + i * logt + (n-i) * logt1) end
- return sum;
- end
-end
-
--- Description: Fisher's exact test
--- Dependent on: math.lbinom()
--- Return: left-, right- and two-tail P-values
---[[
- Fisher's exact test for 2x2 congintency tables:
-
- n11 n12 | n1_
- n21 n22 | n2_
- -----------+----
- n_1 n_2 | n
-
- Reference: http://www.langsrud.com/fisher.htm
-]]--
-function math.fisher_exact(n11, n12, n21, n22)
- local aux; -- keep the states of n* for acceleration
-
- -- Description: hypergeometric function
- local function hypergeo(n11, n1_, n_1, n)
- return math.exp(math.lbinom(n1_, n11) + math.lbinom(n-n1_, n_1-n11) - math.lbinom(n, n_1));
- end
-
- -- Description: incremental hypergeometric function
- -- Note: aux = {n11, n1_, n_1, n, p}
- local function hypergeo_inc(n11, n1_, n_1, n)
- if n1_ ~= 0 or n_1 ~= 0 or n ~= 0 then
- aux = {n11, n1_, n_1, n, 1};
- else -- then only n11 is changed
- local mod;
- _, mod = math.modf(n11 / 11);
- if mod ~= 0 and n11 + aux[4] - aux[2] - aux[3] ~= 0 then
- if n11 == aux[1] + 1 then -- increase by 1
- aux[5] = aux[5] * (aux[2] - aux[1]) / n11 * (aux[3] - aux[1]) / (n11 + aux[4] - aux[2] - aux[3]);
- aux[1] = n11;
- return aux[5];
- end
- if n11 == aux[1] - 1 then -- descrease by 1
- aux[5] = aux[5] * aux[1] / (aux[2] - n11) * (aux[1] + aux[4] - aux[2] - aux[3]) / (aux[3] - n11);
- aux[1] = n11;
- return aux[5];
- end
- end
- aux[1] = n11;
- end
- aux[5] = hypergeo(aux[1], aux[2], aux[3], aux[4]);
- return aux[5];
- end
-
- -- Description: computing the P-value by Fisher's exact test
- local max, min, left, right, n1_, n_1, n, two, p, q, i, j;
- n1_, n_1, n = n11 + n12, n11 + n21, n11 + n12 + n21 + n22;
- max = (n_1 < n1_ and n_1) or n1_; -- max n11, for the right tail
- min = n1_ + n_1 - n;
- if min < 0 then min = 0 end -- min n11, for the left tail
- two, left, right = 1, 1, 1;
- if min == max then return 1 end -- no need to do test
- q = hypergeo_inc(n11, n1_, n_1, n); -- the probability of the current table
- -- left tail
- i, left, p = min + 1, 0, hypergeo_inc(min, 0, 0, 0);
- while p < 0.99999999 * q do
- left, p, i = left + p, hypergeo_inc(i, 0, 0, 0), i + 1;
- end
- i = i - 1;
- if p < 1.00000001 * q then left = left + p;
- else i = i - 1 end
- -- right tail
- j, right, p = max - 1, 0, hypergeo_inc(max, 0, 0, 0);
- while p < 0.99999999 * q do
- right, p, j = right + p, hypergeo_inc(j, 0, 0, 0), j - 1;
- end
- j = j + 1;
- if p < 1.00000001 * q then right = right + p;
- else j = j + 1 end
- -- two-tail
- two = left + right;
- if two > 1 then two = 1 end
- -- adjust left and right
- if math.abs(i - n11) < math.abs(j - n11) then right = 1 - left + q;
- else left = 1 - right + q end
- return left, right, two;
-end
-
--- Description: Delete-m Jackknife
---[[
- Given g groups of values with a statistics estimated from m[i] samples in
- i-th group being t[i], compute the mean and the variance. t0 below is the
- estimate from all samples. Reference:
-
- Busing et al. (1999) Delete-m Jackknife for unequal m. Statistics and Computing, 9:3-8.
-]]--
-function math.jackknife(g, m, t, t0)
- local h, n, sum = {}, 0, 0;
- for j = 1, g do n = n + m[j] end
- if t0 == nil then -- When t0 is absent, estimate it in a naive way
- t0 = 0;
- for j = 1, g do t0 = t0 + m[j] * t[j] end
- t0 = t0 / n;
- end
- local mean, var = 0, 0;
- for j = 1, g do
- h[j] = n / m[j];
- mean = mean + (1 - m[j] / n) * t[j];
- end
- mean = g * t0 - mean; -- Eq. (8)
- for j = 1, g do
- local x = h[j] * t0 - (h[j] - 1) * t[j] - mean;
- var = var + 1 / (h[j] - 1) * x * x;
- end
- var = var / g;
- return mean, var;
-end
-
--- Description: Pearson correlation coefficient
--- Input: a is an n*2 table
-function math.pearson(a)
- -- compute the mean
- local x1, y1 = 0, 0
- for _, v in pairs(a) do
- x1, y1 = x1 + v[1], y1 + v[2]
- end
- -- compute the coefficient
- x1, y1 = x1 / #a, y1 / #a
- local x2, y2, xy = 0, 0, 0
- for _, v in pairs(a) do
- local tx, ty = v[1] - x1, v[2] - y1
- xy, x2, y2 = xy + tx * ty, x2 + tx * tx, y2 + ty * ty
- end
- return xy / math.sqrt(x2) / math.sqrt(y2)
-end
-
--- Description: Spearman correlation coefficient
-function math.spearman(a)
- local function aux_func(t) -- auxiliary function
- return (t == 1 and 0) or (t*t - 1) * t / 12
- end
-
- for _, v in pairs(a) do v.r = {} end
- local T, S = {}, {}
- -- compute the rank
- for k = 1, 2 do
- table.sort(a, function(u,v) return u[k]<v[k] end)
- local same = 1
- T[k] = 0
- for i = 2, #a + 1 do
- if i <= #a and a[i-1][k] == a[i][k] then same = same + 1
- else
- local rank = (i-1) * 2 - same + 1
- for j = i - same, i - 1 do a[j].r[k] = rank end
- if same > 1 then T[k], same = T[k] + aux_func(same), 1 end
- end
- end
- S[k] = aux_func(#a) - T[k]
- end
- -- compute the coefficient
- local sum = 0
- for _, v in pairs(a) do -- TODO: use nested loops to reduce loss of precision
- local t = (v.r[1] - v.r[2]) / 2
- sum = sum + t * t
- end
- return (S[1] + S[2] - sum) / 2 / math.sqrt(S[1] * S[2])
-end
-
--- Description: Hooke-Jeeves derivative-free optimization
-function math.fmin(func, x, data, r, eps, max_calls)
- local n, n_calls = #x, 0;
- r = r or 0.5;
- eps = eps or 1e-7;
- max_calls = max_calls or 50000
-
- function fmin_aux(x1, data, fx1, dx) -- auxiliary function
- local ftmp;
- for k = 1, n do
- x1[k] = x1[k] + dx[k];
- local ftmp = func(x1, data); n_calls = n_calls + 1;
- if ftmp < fx1 then fx1 = ftmp;
- else -- search the opposite direction
- dx[k] = -dx[k];
- x1[k] = x1[k] + dx[k] + dx[k];
- ftmp = func(x1, data); n_calls = n_calls + 1;
- if ftmp < fx1 then fx1 = ftmp
- else x1[k] = x1[k] - dx[k] end -- back to the original x[k]
- end
- end
- return fx1; -- here: fx1=f(n,x1)
- end
-
- local dx, x1 = {}, {};
- for k = 1, n do -- initial directions, based on MGJ
- dx[k] = math.abs(x[k]) * r;
- if dx[k] == 0 then dx[k] = r end;
- end
- local radius = r;
- local fx1, fx;
- fx = func(x, data); fx1 = fx; n_calls = n_calls + 1;
- while true do
- for i = 1, n do x1[i] = x[i] end; -- x1 = x
- fx1 = fmin_aux(x1, data, fx, dx);
- while fx1 < fx do
- for k = 1, n do
- local t = x[k];
- dx[k] = (x1[k] > x[k] and math.abs(dx[k])) or -math.abs(dx[k]);
- x[k] = x1[k];
- x1[k] = x1[k] + x1[k] - t;
- end
- fx = fx1;
- if n_calls >= max_calls then break end
- fx1 = func(x1, data); n_calls = n_calls + 1;
- fx1 = fmin_aux(x1, data, fx1, dx);
- if fx1 >= fx then break end
- local kk = n;
- for k = 1, n do
- if math.abs(x1[k] - x[k]) > .5 * math.abs(dx[k]) then
- kk = k;
- break;
- end
- end
- if kk == n then break end
- end
- if radius >= eps then
- if n_calls >= max_calls then break end
- radius = radius * r;
- for k = 1, n do dx[k] = dx[k] * r end
- else break end
- end
- return fx1, n_calls;
-end
-
---
--- Matrix
---
-
-matrix = {}
-
--- Description: matrix transpose
--- Required by: matrix.mul()
-function matrix.T(a)
- local m, n, x = #a, #a[1], {};
- for i = 1, n do
- x[i] = {};
- for j = 1, m do x[i][j] = a[j][i] end
- end
- return x;
-end
-
--- Description: matrix add
-function matrix.add(a, b)
- assert(#a == #b and #a[1] == #b[1]);
- local m, n, x = #a, #a[1], {};
- for i = 1, m do
- x[i] = {};
- local ai, bi, xi = a[i], b[i], x[i];
- for j = 1, n do xi[j] = ai[j] + bi[j] end
- end
- return x;
-end
-
--- Description: matrix mul
--- Dependent on: matrix.T()
--- Note: much slower without transpose
-function matrix.mul(a, b)
- assert(#a[1] == #b);
- local m, n, p, x = #a, #a[1], #b[1], {};
- local c = matrix.T(b); -- transpose for efficiency
- for i = 1, m do
- x[i] = {}
- local xi = x[i];
- for j = 1, p do
- local sum, ai, cj = 0, a[i], c[j];
- for k = 1, n do sum = sum + ai[k] * cj[k] end
- xi[j] = sum;
- end
- end
- return x;
-end
-
--- Description: matrix print
-function matrix.tostring(a)
- local z = {};
- for i = 1, #a do
- z[i] = table.concat(a[i], "\t");
- end
- return table.concat(z, "\n");
-end
-
--- Description: chi^2 test for contingency tables
--- Dependent on: math.igamma()
-function matrix.chi2(a)
- if #a == 2 and #a[1] == 2 then -- 2x2 table
- local x, z
- x = (a[1][1] + a[1][2]) * (a[2][1] + a[2][2]) * (a[1][1] + a[2][1]) * (a[1][2] + a[2][2])
- if x == 0 then return 0, 1, false end
- z = a[1][1] * a[2][2] - a[1][2] * a[2][1]
- z = (a[1][1] + a[1][2] + a[2][1] + a[2][2]) * z * z / x
- return z, math.igamma(.5, .5 * z, true), true
- else -- generic table
- local rs, cs, n, m, N, z = {}, {}, #a, #a[1], 0, 0
- for i = 1, n do rs[i] = 0 end
- for j = 1, m do cs[j] = 0 end
- for i = 1, n do -- compute column sum and row sum
- for j = 1, m do cs[j], rs[i] = cs[j] + a[i][j], rs[i] + a[i][j] end
- end
- for i = 1, n do N = N + rs[i] end
- for i = 1, n do -- compute the chi^2 statistics
- for j = 1, m do
- local E = rs[i] * cs[j] / N;
- z = z + (a[i][j] - E) * (a[i][j] - E) / E
- end
- end
- return z, math.igamma(.5 * (n-1) * (m-1), .5 * z, true), true;
- end
-end
-
--- Description: Gauss-Jordan elimination (solving equations; computing inverse)
--- Note: on return, a[n][n] is the inverse; b[n][m] is the solution
--- Reference: Section 2.1, Numerical Recipes in C, 2nd edition
-function matrix.solve(a, b)
- assert(#a == #a[1]);
- local n, m = #a, (b and #b[1]) or 0;
- local xc, xr, ipiv = {}, {}, {};
- local ic, ir;
-
- for j = 1, n do ipiv[j] = 0 end
- for i = 1, n do
- local big = 0;
- for j = 1, n do
- local aj = a[j];
- if ipiv[j] ~= 1 then
- for k = 1, n do
- if ipiv[k] == 0 then
- if math.abs(aj[k]) >= big then
- big = math.abs(aj[k]);
- ir, ic = j, k;
- end
- elseif ipiv[k] > 1 then return -2 end -- singular matrix
- end
- end
- end
- ipiv[ic] = ipiv[ic] + 1;
- if ir ~= ic then
- for l = 1, n do a[ir][l], a[ic][l] = a[ic][l], a[ir][l] end
- if b then
- for l = 1, m do b[ir][l], b[ic][l] = b[ic][l], b[ir][l] end
- end
- end
- xr[i], xc[i] = ir, ic;
- if a[ic][ic] == 0 then return -3 end -- singular matrix
- local pivinv = 1 / a[ic][ic];
- a[ic][ic] = 1;
- for l = 1, n do a[ic][l] = a[ic][l] * pivinv end
- if b then
- for l = 1, n do b[ic][l] = b[ic][l] * pivinv end
- end
- for ll = 1, n do
- if ll ~= ic then
- local tmp = a[ll][ic];
- a[ll][ic] = 0;
- local all, aic = a[ll], a[ic];
- for l = 1, n do all[l] = all[l] - aic[l] * tmp end
- if b then
- local bll, bic = b[ll], b[ic];
- for l = 1, m do bll[l] = bll[l] - bic[l] * tmp end
- end
- end
- end
- end
- for l = n, 1, -1 do
- if xr[l] ~= xc[l] then
- for k = 1, n do a[k][xr[l]], a[k][xc[l]] = a[k][xc[l]], a[k][xr[l]] end
- end
- end
- return 0;
-end
diff --git a/debian/vendor-h2o/deps/klib/test/Makefile b/debian/vendor-h2o/deps/klib/test/Makefile
deleted file mode 100644
index a392c8e..0000000
--- a/debian/vendor-h2o/deps/klib/test/Makefile
+++ /dev/null
@@ -1,60 +0,0 @@
-CC=gcc
-CXX=g++
-CFLAGS=-g -Wall -O2 -I..
-CXXFLAGS=$(CFLAGS)
-PROGS=kbtree_test khash_keith khash_keith2 khash_test klist_test kseq_test kseq_bench \
- kseq_bench2 ksort_test ksort_test-stl kvec_test kmin_test kstring_bench kstring_bench2 kstring_test \
- kthread_test
-
-all:$(PROGS)
-
-clean:
- rm -fr $(PROGS) *.dSYM a.out
-
-kbtree_test:kbtree_test.c ../kbtree.h
- $(CC) $(CFLAGS) -o $@ kbtree_test.c
-
-khash_keith:khash_keith.c ../khash.h
- $(CC) $(CFLAGS) -o $@ khash_keith.c
-
-khash_keith2:khash_keith2.c ../khash.h
- $(CC) $(CFLAGS) -o $@ khash_keith2.c
-
-khash_test:khash_test.c ../khash.h
- $(CC) $(CFLAGS) -o $@ khash_test.c
-
-klist_test:klist_test.c ../klist.h
- $(CC) $(CFLAGS) -o $@ klist_test.c
-
-kseq_test:kseq_test.c ../kseq.h
- $(CC) $(CFLAGS) -o $@ kseq_test.c -lz
-
-kseq_bench:kseq_bench.c ../kseq.h
- $(CC) $(CFLAGS) -o $@ kseq_bench.c -lz
-
-kseq_bench2:kseq_bench2.c ../kseq.h
- $(CC) $(CFLAGS) -o $@ kseq_bench2.c -lz
-
-ksort_test:ksort_test.c ../ksort.h
- $(CC) $(CFLAGS) -o $@ ksort_test.c
-
-ksort_test-stl:ksort_test.cc ../ksort.h
- $(CXX) $(CXXFLAGS) -o $@ ksort_test.cc
-
-kvec_test:kvec_test.cc ../kvec.h
- $(CXX) $(CXXFLAGS) -o $@ kvec_test.cc
-
-kmin_test:kmin_test.c ../kmath.h ../kmath.c
- $(CC) $(CFLAGS) -o $@ kmin_test.c ../kmath.c
-
-kstring_bench:kstring_bench.c ../kstring.h ../kstring.c
- $(CC) $(CFLAGS) -o $@ kstring_bench.c ../kstring.c
-
-kstring_bench2:kstring_bench2.c ../kstring.h ../kstring.c
- $(CC) $(CFLAGS) -o $@ kstring_bench2.c ../kstring.c
-
-kstring_test:kstring_test.c ../kstring.h ../kstring.c
- $(CC) $(CFLAGS) -o $@ kstring_test.c ../kstring.c
-
-kthread_test:kthread_test.c ../kthread.c
- $(CC) $(CFLAGS) -fopenmp -o $@ kthread_test.c ../kthread.c
diff --git a/debian/vendor-h2o/deps/klib/test/kbit_test.c b/debian/vendor-h2o/deps/klib/test/kbit_test.c
deleted file mode 100644
index 3ae3bd3..0000000
--- a/debian/vendor-h2o/deps/klib/test/kbit_test.c
+++ /dev/null
@@ -1,137 +0,0 @@
-#include <stdlib.h>
-#include <stdio.h>
-#include <time.h>
-#include <emmintrin.h>
-#include "kbit.h"
-
-// from bowtie-0.9.8.1
-inline static int bt1_pop64(uint64_t x) // the kbi_popcount64() equivalence; similar to popcount_2() in wiki
-{
- x -= ((x >> 1) & 0x5555555555555555llu);
- x = (x & 0x3333333333333333llu) + ((x >> 2) & 0x3333333333333333llu);
- x = (x + (x >> 4)) & 0x0F0F0F0F0F0F0F0Fllu;
- x = x + (x >> 8);
- x = x + (x >> 16);
- x = x + (x >> 32);
- return x & 0x3F;
-}
-
-inline static int bt1_countInU64(uint64_t dw, int c) // the kbi_DNAcount64() equivalence
-{
- uint64_t dwA = dw & 0xAAAAAAAAAAAAAAAAllu;
- uint64_t dwNA = dw & ~0xAAAAAAAAAAAAAAAAllu;
- uint64_t tmp;
- switch (c) {
- case 0: tmp = (dwA >> 1) | dwNA; break;
- case 1: tmp = ~(dwA >> 1) & dwNA; break;
- case 2: tmp = (dwA >> 1) & ~dwNA; break;
- default: tmp = (dwA >> 1) & dwNA;
- }
- tmp = bt1_pop64(tmp);
- if (c == 0) tmp = 32 - tmp;
- return (int)tmp;
-}
-
-// from bigmagic
-static uint32_t sse2_bit_count32(const __m128i* block, const __m128i* block_end)
-{
- const unsigned mu1 = 0x55555555;
- const unsigned mu2 = 0x33333333;
- const unsigned mu3 = 0x0F0F0F0F;
- const unsigned mu4 = 0x0000003F;
-
- uint32_t tcnt[4];
-
- // Loading masks
- __m128i m1 = _mm_set_epi32 (mu1, mu1, mu1, mu1);
- __m128i m2 = _mm_set_epi32 (mu2, mu2, mu2, mu2);
- __m128i m3 = _mm_set_epi32 (mu3, mu3, mu3, mu3);
- __m128i m4 = _mm_set_epi32 (mu4, mu4, mu4, mu4);
- __m128i mcnt;
- mcnt = _mm_xor_si128(m1, m1); // cnt = 0
-
- __m128i tmp1, tmp2;
- do
- {
- __m128i b = _mm_load_si128(block);
- ++block;
-
- // b = (b & 0x55555555) + (b >> 1 & 0x55555555);
- tmp1 = _mm_srli_epi32(b, 1); // tmp1 = (b >> 1 & 0x55555555)
- tmp1 = _mm_and_si128(tmp1, m1);
- tmp2 = _mm_and_si128(b, m1); // tmp2 = (b & 0x55555555)
- b = _mm_add_epi32(tmp1, tmp2); // b = tmp1 + tmp2
-
- // b = (b & 0x33333333) + (b >> 2 & 0x33333333);
- tmp1 = _mm_srli_epi32(b, 2); // (b >> 2 & 0x33333333)
- tmp1 = _mm_and_si128(tmp1, m2);
- tmp2 = _mm_and_si128(b, m2); // (b & 0x33333333)
- b = _mm_add_epi32(tmp1, tmp2); // b = tmp1 + tmp2
-
- // b = (b + (b >> 4)) & 0x0F0F0F0F;
- tmp1 = _mm_srli_epi32(b, 4); // tmp1 = b >> 4
- b = _mm_add_epi32(b, tmp1); // b = b + (b >> 4)
- b = _mm_and_si128(b, m3); // & 0x0F0F0F0F
-
- // b = b + (b >> 8);
- tmp1 = _mm_srli_epi32 (b, 8); // tmp1 = b >> 8
- b = _mm_add_epi32(b, tmp1); // b = b + (b >> 8)
-
- // b = (b + (b >> 16)) & 0x0000003F;
- tmp1 = _mm_srli_epi32 (b, 16); // b >> 16
- b = _mm_add_epi32(b, tmp1); // b + (b >> 16)
- b = _mm_and_si128(b, m4); // (b >> 16) & 0x0000003F;
-
- mcnt = _mm_add_epi32(mcnt, b); // mcnt += b
-
- } while (block < block_end);
-
- _mm_store_si128((__m128i*)tcnt, mcnt);
-
- return tcnt[0] + tcnt[1] + tcnt[2] + tcnt[3];
-}
-
-int main(void)
-{
- int i, N = 100000000;
- uint64_t *x, cnt;
- clock_t t;
- int c = 1;
-
- x = (uint64_t*)calloc(N, 8);
- srand48(11);
- for (i = 0; i < N; ++i)
- x[i] = (uint64_t)lrand48() << 32 ^ lrand48();
-
- fprintf(stderr, "\n===> Calculate # of 1 in an integer (popcount) <===\n");
-
- t = clock(); cnt = 0;
- for (i = 0; i < N; ++i) cnt += kbi_popcount64(x[i]);
- fprintf(stderr, "%20s\t%20ld\t%10.6f\n", "kbit", (long)cnt, (double)(clock() - t) / CLOCKS_PER_SEC);
-
- t = clock(); cnt = 0;
- for (i = 0; i < N; ++i) cnt += bt1_pop64(x[i]);
- fprintf(stderr, "%20s\t%20ld\t%10.6f\n", "wiki-popcount_2", (long)cnt, (double)(clock() - t) / CLOCKS_PER_SEC);
-
- t = clock(); cnt = 0;
- for (i = 0; i < N; ++i) cnt += __builtin_popcountl(x[i]);
- fprintf(stderr, "%20s\t%20ld\t%10.6f\n", "__builtin_popcountl", (long)cnt, (double)(clock() - t) / CLOCKS_PER_SEC);
-
- t = clock(); cnt = 0;
- cnt += sse2_bit_count32((__m128i*)x, (__m128i*)(x+N));
- fprintf(stderr, "%20s\t%20ld\t%10.6f\n", "SSE2-32bit", (long)cnt, (double)(clock() - t) / CLOCKS_PER_SEC);
-
- fprintf(stderr, "\n===> Count '%c' in 2-bit encoded integers <===\n", "ACGT"[c]);
-
- t = clock(); cnt = 0;
- for (i = 0; i < N; ++i) cnt += kbi_DNAcount64(x[i], c);
- fprintf(stderr, "%20s\t%20ld\t%10.6f\n", "kbit", (long)cnt, (double)(clock() - t) / CLOCKS_PER_SEC);
-
- t = clock(); cnt = 0;
- for (i = 0; i < N; ++i) cnt += bt1_countInU64(x[i], c);
- fprintf(stderr, "%20s\t%20ld\t%10.6f\n", "bowtie1", (long)cnt, (double)(clock() - t) / CLOCKS_PER_SEC);
-
- fprintf(stderr, "\n");
- free(x);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kbtree_test.c b/debian/vendor-h2o/deps/klib/test/kbtree_test.c
deleted file mode 100644
index 8e10687..0000000
--- a/debian/vendor-h2o/deps/klib/test/kbtree_test.c
+++ /dev/null
@@ -1,94 +0,0 @@
-#include <stdio.h>
-#include <assert.h>
-#include <time.h>
-#include <stdlib.h>
-#include <stdint.h>
-#include <string.h>
-
-typedef const char *str_t;
-
-#include "kbtree.h"
-KBTREE_INIT(int, uint32_t, kb_generic_cmp)
-KBTREE_INIT(str, str_t, kb_str_cmp)
-
-static int data_size = 5000000;
-static unsigned *int_data;
-static char **str_data;
-
-void ht_init_data()
-{
- int i;
- char buf[256];
- printf("--- generating data... ");
- srand48(11);
- int_data = (unsigned*)calloc(data_size, sizeof(unsigned));
- str_data = (char**)calloc(data_size, sizeof(char*));
- for (i = 0; i < data_size; ++i) {
- int_data[i] = (unsigned)(data_size * drand48() / 4) * 271828183u;
- sprintf(buf, "%x", int_data[i]);
- str_data[i] = strdup(buf);
- }
- printf("done!\n");
-}
-void ht_destroy_data()
-{
- int i;
- for (i = 0; i < data_size; ++i) free(str_data[i]);
- free(str_data); free(int_data);
-}
-
-void ht_khash_int()
-{
- int i;
- unsigned *data = int_data;
- uint32_t *l, *u;
- kbtree_t(int) *h;
-
- h = kb_init(int, KB_DEFAULT_SIZE);
- for (i = 0; i < data_size; ++i) {
- if (kb_get(int, h, data[i]) == 0) kb_put(int, h, data[i]);
- else kb_del(int, h, data[i]);
- }
- printf("[ht_khash_int] size: %d\n", kb_size(h));
- if (1) {
- int cnt = 0;
- uint32_t x, y;
- kb_interval(int, h, 2174625464u, &l, &u);
- printf("interval for 2174625464: (%u, %u)\n", l? *l : 0, u? *u : 0);
-#define traverse_f(p) { if (cnt == 0) y = *p; ++cnt; }
- __kb_traverse(uint32_t, h, traverse_f);
- __kb_get_first(uint32_t, h, x);
- printf("# of elements from traversal: %d\n", cnt);
- printf("first element: %d == %d\n", x, y);
- }
- __kb_destroy(h);
-}
-void ht_khash_str()
-{
- int i;
- char **data = str_data;
- kbtree_t(str) *h;
-
- h = kb_init(str, KB_DEFAULT_SIZE);
- for (i = 0; i < data_size; ++i) {
- if (kb_get(str, h, data[i]) == 0) kb_put(str, h, data[i]);
- else kb_del(str, h, data[i]);
- }
- printf("[ht_khash_int] size: %d\n", kb_size(h));
- __kb_destroy(h);
-}
-void ht_timing(void (*f)(void))
-{
- clock_t t = clock();
- (*f)();
- printf("[ht_timing] %.3lf sec\n", (double)(clock() - t) / CLOCKS_PER_SEC);
-}
-int main(int argc, char *argv[])
-{
- if (argc > 1) data_size = atoi(argv[1]);
- ht_init_data();
- ht_timing(ht_khash_int);
- ht_timing(ht_khash_str);
- ht_destroy_data();
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kgraph_test.c b/debian/vendor-h2o/deps/klib/test/kgraph_test.c
deleted file mode 100644
index 3da1cd7..0000000
--- a/debian/vendor-h2o/deps/klib/test/kgraph_test.c
+++ /dev/null
@@ -1,26 +0,0 @@
-#include <stdio.h>
-#include "kgraph.h"
-
-KHASH_INIT2(e32, extern, uint32_t, int, 1, kh_int_hash_func, kh_int_hash_equal)
-
-typedef struct {
- int i;
- khash_t(e32) *_arc;
-} vertex_t;
-
-KGRAPH_INIT(g, extern, vertex_t, int, e32)
-KGRAPH_PRINT(g, extern)
-
-int main()
-{
- int *pb, *pe;
- kgraph_t(g) *g;
- g = kg_init_g();
- kg_put_a_g(g, 10, 20, 0, &pb, &pe);
- kg_put_a_g(g, 20, 30, 0, &pb, &pe);
- kg_put_a_g(g, 30, 10, 1, &pb, &pe);
- kg_del_v_g(g, 20);
- kg_print_g(g);
- kg_destroy_g(g);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/khash_keith.c b/debian/vendor-h2o/deps/klib/test/khash_keith.c
deleted file mode 100644
index ddd755a..0000000
--- a/debian/vendor-h2o/deps/klib/test/khash_keith.c
+++ /dev/null
@@ -1,95 +0,0 @@
-/*
- * This is an optimized version of the following C++ program:
- *
- * http://keithlea.com/javabench/src/cpp/hash.cpp
- *
- * Keith in his benchmark (http://keithlea.com/javabench/data) showed that the
- * Java implementation is twice as fast as the C++ version. In fact, this is
- * only because the C++ implementation is substandard. Most importantly, Keith
- * is using "sprintf()" to convert an integer to a string, which is known to be
- * extremely inefficient.
- */
-#include <stdio.h>
-#include "khash.h"
-KHASH_MAP_INIT_STR(str, int)
-
-inline void int2str(int c, int base, char *ret)
-{
- const char *tab = "0123456789abcdef";
- if (c == 0) ret[0] = '0', ret[1] = 0;
- else {
- int l, x, y;
- char buf[16];
- for (l = 0, x = c < 0? -c : c; x > 0; x /= base) buf[l++] = tab[x%base];
- if (c < 0) buf[l++] = '-';
- for (x = l - 1, y = 0; x >= 0; --x) ret[y++] = buf[x];
- ret[y] = 0;
- }
-}
-
-#ifndef _USE_STRDUP
-#define BLOCK_SIZE 0x100000
-int main(int argc, char *argv[])
-{
- char **mem = 0;
- int i, l, n = 1000000, ret, block_end = 0, curr = 0, c = 0;
- khash_t(str) *h;
- h = kh_init(str);
- if (argc > 1) n = atoi(argv[1]);
- mem = malloc(sizeof(void*));
- mem[0] = malloc(BLOCK_SIZE); // memory buffer to avoid memory fragmentation
- curr = block_end = 0;
- for (i = 1; i <= n; ++i) {
- char buf[16];
- int2str(i, 16, buf);
- khint_t k = kh_put(str, h, buf, &ret);
- l = strlen(buf) + 1;
- if (block_end + l > BLOCK_SIZE) {
- ++curr; block_end = 0;
- mem = realloc(mem, (curr + 1) * sizeof(void*));
- mem[curr] = malloc(BLOCK_SIZE);
- }
- memcpy(mem[curr] + block_end, buf, l);
- kh_key(h, k) = mem[curr] + block_end;
- block_end += l;
- kh_val(h, k) = i;
- }
- for (i = 1; i <= n; ++i) {
- char buf[16];
- int2str(i, 10, buf);
- khint_t k = kh_get(str, h, buf);
- if (k != kh_end(h)) ++c;
- }
- printf("%d\n", c);
- for (ret = 0; ret <= curr; ++ret) free(mem[ret]);
- free(mem);
- kh_destroy(str, h);
- return 0;
-}
-#else // _USE_STRDUP
-int main(int argc, char *argv[])
-{
- int i, l, n = 1000000, ret, c = 0;
- khash_t(str) *h;
- khint_t k;
- h = kh_init(str);
- if (argc > 1) n = atoi(argv[1]);
- for (i = 1; i <= n; ++i) {
- char buf[16];
- int2str(i, 16, buf);
- k = kh_put(str, h, strdup(buf), &ret);
- kh_val(h, k) = i;
- }
- for (i = 1; i <= n; ++i) {
- char buf[16];
- int2str(i, 10, buf);
- k = kh_get(str, h, buf);
- if (k != kh_end(h)) ++c;
- }
- for (k = kh_begin(h); k != kh_end(h); ++k) // explicitly freeing memory takes 10-20% CPU time.
- if (kh_exist(h, k)) free((char*)kh_key(h, k));
- printf("%d\n", c);
- kh_destroy(str, h);
- return 0;
-}
-#endif
diff --git a/debian/vendor-h2o/deps/klib/test/khash_keith2.c b/debian/vendor-h2o/deps/klib/test/khash_keith2.c
deleted file mode 100644
index b9df9b7..0000000
--- a/debian/vendor-h2o/deps/klib/test/khash_keith2.c
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * This is an optimized version of the following C++ program:
- *
- * http://keithlea.com/javabench/src/cpp/hash.cpp
- *
- * Keith in his benchmark (http://keithlea.com/javabench/data) showed that the
- * Java implementation is twice as fast as the C++ version. In fact, this is
- * only because the C++ implementation is substandard. Most importantly, Keith
- * is using "sprintf()" to convert an integer to a string, which is known to be
- * extremely inefficient.
- */
-#include <stdio.h>
-#include "khash.h"
-KHASH_MAP_INIT_STR(str, int)
-
-inline void int2str(int c, int base, char *ret)
-{
- const char *tab = "0123456789abcdef";
- if (c == 0) ret[0] = '0', ret[1] = 0;
- else {
- int l, x, y;
- char buf[16];
- for (l = 0, x = c < 0? -c : c; x > 0; x /= base) buf[l++] = tab[x%base];
- if (c < 0) buf[l++] = '-';
- for (x = l - 1, y = 0; x >= 0; --x) ret[y++] = buf[x];
- ret[y] = 0;
- }
-}
-
-int main(int argc, char *argv[])
-{
- int i, l, n = 1000, ret;
- khash_t(str) *h, *h2;
- khint_t k;
- h = kh_init(str);
- h2 = kh_init(str);
- if (argc > 1) n = atoi(argv[1]);
- for (i = 0; i < 10000; ++i) {
- char buf[32];
- strcpy(buf, "foo_");
- int2str(i, 10, buf+4);
- k = kh_put(str, h, strdup(buf), &ret);
- kh_val(h, k) = i;
- }
- for (i = 0; i < n; ++i) {
- for (k = kh_begin(h); k != kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- khint_t k2 = kh_put(str, h2, kh_key(h, k), &ret);
- if (ret) { // absent
- kh_key(h2, k2) = strdup(kh_key(h, k));
- kh_val(h2, k2) = kh_val(h, k);
- } else kh_val(h2, k2) += kh_val(h, k);
- }
- }
- }
- k = kh_get(str, h, "foo_1"); printf("%d", kh_val(h, k));
- k = kh_get(str, h, "foo_9999"); printf(" %d", kh_val(h, k));
- k = kh_get(str, h2, "foo_1"); printf(" %d", kh_val(h2, k));
- k = kh_get(str, h2, "foo_9999"); printf(" %d\n", kh_val(h2, k));
- for (k = kh_begin(h); k != kh_end(h); ++k)
- if (kh_exist(h, k)) free((char*)kh_key(h, k));
- for (k = kh_begin(h2); k != kh_end(h2); ++k)
- if (kh_exist(h2, k)) free((char*)kh_key(h2, k));
- kh_destroy(str, h);
- kh_destroy(str, h2);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/khash_test.c b/debian/vendor-h2o/deps/klib/test/khash_test.c
deleted file mode 100644
index 8d6687f..0000000
--- a/debian/vendor-h2o/deps/klib/test/khash_test.c
+++ /dev/null
@@ -1,141 +0,0 @@
-#include <stdio.h>
-#include <assert.h>
-#include <time.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "khash.h"
-KHASH_SET_INIT_STR(str)
-KHASH_MAP_INIT_INT(int, unsigned char)
-
-typedef struct {
- unsigned key;
- unsigned char val;
-} int_unpack_t;
-
-typedef struct {
- unsigned key;
- unsigned char val;
-} __attribute__ ((__packed__)) int_packed_t;
-
-#define hash_eq(a, b) ((a).key == (b).key)
-#define hash_func(a) ((a).key)
-
-KHASH_INIT(iun, int_unpack_t, char, 0, hash_func, hash_eq)
-KHASH_INIT(ipk, int_packed_t, char, 0, hash_func, hash_eq)
-
-static int data_size = 5000000;
-static unsigned *int_data;
-static char **str_data;
-
-void ht_init_data()
-{
- int i;
- char buf[256];
- khint32_t x = 11;
- printf("--- generating data... ");
- int_data = (unsigned*)calloc(data_size, sizeof(unsigned));
- str_data = (char**)calloc(data_size, sizeof(char*));
- for (i = 0; i < data_size; ++i) {
- int_data[i] = (unsigned)(data_size * ((double)x / UINT_MAX) / 4) * 271828183u;
- sprintf(buf, "%x", int_data[i]);
- str_data[i] = strdup(buf);
- x = 1664525L * x + 1013904223L;
- }
- printf("done!\n");
-}
-
-void ht_destroy_data()
-{
- int i;
- for (i = 0; i < data_size; ++i) free(str_data[i]);
- free(str_data); free(int_data);
-}
-
-void ht_khash_int()
-{
- int i, ret;
- unsigned *data = int_data;
- khash_t(int) *h;
- unsigned k;
-
- h = kh_init(int);
- for (i = 0; i < data_size; ++i) {
- k = kh_put(int, h, data[i], &ret);
- kh_val(h, k) = i&0xff;
- if (!ret) kh_del(int, h, k);
- }
- printf("[ht_khash_int] size: %u\n", kh_size(h));
- kh_destroy(int, h);
-}
-
-void ht_khash_str()
-{
- int i, ret;
- char **data = str_data;
- khash_t(str) *h;
- unsigned k;
-
- h = kh_init(str);
- for (i = 0; i < data_size; ++i) {
- k = kh_put(str, h, data[i], &ret);
- if (!ret) kh_del(str, h, k);
- }
- printf("[ht_khash_int] size: %u\n", kh_size(h));
- kh_destroy(str, h);
-}
-
-void ht_khash_unpack()
-{
- int i, ret;
- unsigned *data = int_data;
- khash_t(iun) *h;
- unsigned k;
-
- h = kh_init(iun);
- for (i = 0; i < data_size; ++i) {
- int_unpack_t x;
- x.key = data[i]; x.val = i&0xff;
- k = kh_put(iun, h, x, &ret);
- if (!ret) kh_del(iun, h, k);
- }
- printf("[ht_khash_unpack] size: %u (sizeof=%ld)\n", kh_size(h), sizeof(int_unpack_t));
- kh_destroy(iun, h);
-}
-
-void ht_khash_packed()
-{
- int i, ret;
- unsigned *data = int_data;
- khash_t(ipk) *h;
- unsigned k;
-
- h = kh_init(ipk);
- for (i = 0; i < data_size; ++i) {
- int_packed_t x;
- x.key = data[i]; x.val = i&0xff;
- k = kh_put(ipk, h, x, &ret);
- if (!ret) kh_del(ipk, h, k);
- }
- printf("[ht_khash_packed] size: %u (sizeof=%ld)\n", kh_size(h), sizeof(int_packed_t));
- kh_destroy(ipk, h);
-}
-
-void ht_timing(void (*f)(void))
-{
- clock_t t = clock();
- (*f)();
- printf("[ht_timing] %.3lf sec\n", (double)(clock() - t) / CLOCKS_PER_SEC);
-}
-
-int main(int argc, char *argv[])
-{
- if (argc > 1) data_size = atoi(argv[1]);
- ht_init_data();
- ht_timing(ht_khash_int);
- ht_timing(ht_khash_str);
- ht_timing(ht_khash_unpack);
- ht_timing(ht_khash_packed);
- ht_destroy_data();
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/klist_test.c b/debian/vendor-h2o/deps/klib/test/klist_test.c
deleted file mode 100644
index cd13813..0000000
--- a/debian/vendor-h2o/deps/klib/test/klist_test.c
+++ /dev/null
@@ -1,19 +0,0 @@
-#include <stdio.h>
-#include "klist.h"
-
-#define __int_free(x)
-KLIST_INIT(32, int, __int_free)
-
-int main()
-{
- klist_t(32) *kl;
- kliter_t(32) *p;
- kl = kl_init(32);
- *kl_pushp(32, kl) = 1;
- *kl_pushp(32, kl) = 10;
- kl_shift(32, kl, 0);
- for (p = kl_begin(kl); p != kl_end(kl); p = kl_next(p))
- printf("%d\n", kl_val(p));
- kl_destroy(32, kl);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kmin_test.c b/debian/vendor-h2o/deps/klib/test/kmin_test.c
deleted file mode 100644
index 33ccd1c..0000000
--- a/debian/vendor-h2o/deps/klib/test/kmin_test.c
+++ /dev/null
@@ -1,48 +0,0 @@
-#include <stdio.h>
-#include <math.h>
-#include "kmath.h"
-
-static int n_evals;
-
-double f_Chebyquad(int n, double *x, void *data)
-{
- int i, j;
- double y[20][20], f;
- int np, iw;
- double sum;
- for (j = 0; j != n; ++j) {
- y[0][j] = 1.;
- y[1][j] = 2. * x[j] - 1.;
- }
- for (i = 1; i != n; ++i)
- for (j = 0; j != n; ++j)
- y[i+1][j] = 2. * y[1][j] * y[i][j] - y[i-1][j];
- f = 0.;
- np = n + 1;
- iw = 1;
- for (i = 0; i != np; ++i) {
- sum = 0.;
- for (j = 0; j != n; ++j) sum += y[i][j];
- sum /= n;
- if (iw > 0) sum += 1. / ((i - 1) * (i + 1));
- iw = -iw;
- f += sum * sum;
- }
- ++n_evals;
- return f;
-}
-
-int main()
-{
- double x[20], y;
- int n, i;
- printf("\nMinimizer: Hooke-Jeeves\n");
- for (n = 2; n <= 8; n += 2) {
- for (i = 0; i != n; ++i) x[i] = (double)(i + 1) / n;
- n_evals = 0;
- y = kmin_hj(f_Chebyquad, n, x, 0, KMIN_RADIUS, KMIN_EPS, KMIN_MAXCALL);
- printf("n=%d,min=%.8lg,n_evals=%d\n", n, y, n_evals);
- }
- printf("\n");
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kseq_bench.c b/debian/vendor-h2o/deps/klib/test/kseq_bench.c
deleted file mode 100644
index eeda13f..0000000
--- a/debian/vendor-h2o/deps/klib/test/kseq_bench.c
+++ /dev/null
@@ -1,69 +0,0 @@
-#include <zlib.h>
-#include <stdio.h>
-#include <time.h>
-#include <stdint.h>
-#include <stdlib.h>
-#include "kseq.h"
-
-#define BUF_SIZE 4096
-KSTREAM_INIT(gzFile, gzread, BUF_SIZE)
-
-int main(int argc, char *argv[])
-{
- gzFile fp;
- clock_t t;
- if (argc == 1) {
- fprintf(stderr, "Usage: kseq_bench <in.gz>\n");
- return 1;
- }
- {
- uint8_t *buf = malloc(BUF_SIZE);
- fp = gzopen(argv[1], "r");
- t = clock();
- while (gzread(fp, buf, BUF_SIZE) > 0);
- fprintf(stderr, "[gzread] %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- gzclose(fp);
- free(buf);
- }
- {
- kstream_t *ks;
- fp = gzopen(argv[1], "r");
- ks = ks_init(fp);
- t = clock();
- while (ks_getc(ks) >= 0);
- fprintf(stderr, "[ks_getc] %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- ks_destroy(ks);
- gzclose(fp);
- }
- {
- kstream_t *ks;
- kstring_t *s;
- int dret;
- s = calloc(1, sizeof(kstring_t));
- fp = gzopen(argv[1], "r");
- ks = ks_init(fp);
- t = clock();
- while (ks_getuntil(ks, '\n', s, &dret) >= 0);
- fprintf(stderr, "[ks_getuntil] %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- ks_destroy(ks);
- gzclose(fp);
- free(s->s); free(s);
- }
- if (argc == 2) {
- fp = gzopen(argv[1], "r");
- t = clock();
- while (gzgetc(fp) >= 0);
- fprintf(stderr, "[gzgetc] %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- gzclose(fp);
- }
- if (argc == 2) {
- char *buf = malloc(BUF_SIZE);
- fp = gzopen(argv[1], "r");
- t = clock();
- while (gzgets(fp, buf, BUF_SIZE) > 0);
- fprintf(stderr, "[gzgets] %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- gzclose(fp);
- free(buf);
- }
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kseq_bench2.c b/debian/vendor-h2o/deps/klib/test/kseq_bench2.c
deleted file mode 100644
index b415458..0000000
--- a/debian/vendor-h2o/deps/klib/test/kseq_bench2.c
+++ /dev/null
@@ -1,43 +0,0 @@
-#include <stdio.h>
-#include <time.h>
-#include <stdint.h>
-#include <stdlib.h>
-#include <fcntl.h>
-#include "kseq.h"
-KSTREAM_INIT(int, read, 4096)
-
-#define BUF_SIZE 65536
-
-int main(int argc, char *argv[])
-{
- clock_t t;
- if (argc == 1) {
- fprintf(stderr, "Usage: %s <in.txt>\n", argv[0]);
- return 1;
- }
- {
- FILE *fp;
- char *s;
- t = clock();
- s = malloc(BUF_SIZE);
- fp = fopen(argv[1], "r");
- while (fgets(s, BUF_SIZE, fp));
- fclose(fp);
- fprintf(stderr, "[fgets] %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
- {
- int fd, dret;
- kstream_t *ks;
- kstring_t s;
- t = clock();
- s.l = s.m = 0; s.s = 0;
- fd = open(argv[1], O_RDONLY);
- ks = ks_init(fd);
- while (ks_getuntil(ks, '\n', &s, &dret) >= 0);
- free(s.s);
- ks_destroy(ks);
- close(fd);
- fprintf(stderr, "[kstream] %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kseq_test.c b/debian/vendor-h2o/deps/klib/test/kseq_test.c
deleted file mode 100644
index 0304dea..0000000
--- a/debian/vendor-h2o/deps/klib/test/kseq_test.c
+++ /dev/null
@@ -1,27 +0,0 @@
-#include <zlib.h>
-#include <stdio.h>
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
-
-int main(int argc, char *argv[])
-{
- gzFile fp;
- kseq_t *seq;
- int l;
- if (argc == 1) {
- fprintf(stderr, "Usage: %s <in.fasta>\n", argv[0]);
- return 1;
- }
- fp = gzopen(argv[1], "r");
- seq = kseq_init(fp);
- while ((l = kseq_read(seq)) >= 0) {
- printf("name: %s\n", seq->name.s);
- if (seq->comment.l) printf("comment: %s\n", seq->comment.s);
- printf("seq: %s\n", seq->seq.s);
- if (seq->qual.l) printf("qual: %s\n", seq->qual.s);
- }
- printf("return value: %d\n", l);
- kseq_destroy(seq);
- gzclose(fp);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kseq_test.dat b/debian/vendor-h2o/deps/klib/test/kseq_test.dat
deleted file mode 100644
index b774ae2..0000000
--- a/debian/vendor-h2o/deps/klib/test/kseq_test.dat
+++ /dev/null
@@ -1,12 +0,0 @@
->1
-acgtacgtacgtagc
->2 test
-acgatcgatc
-@3 test2
-cgctagcatagc
-cgatatgactta
-+
-78wo82usd980
-d88fau
-
-238ud8
diff --git a/debian/vendor-h2o/deps/klib/test/ksort_test.c b/debian/vendor-h2o/deps/klib/test/ksort_test.c
deleted file mode 100644
index 92c7d3d..0000000
--- a/debian/vendor-h2o/deps/klib/test/ksort_test.c
+++ /dev/null
@@ -1,104 +0,0 @@
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-#include <time.h>
-#include "ksort.h"
-
-KSORT_INIT_GENERIC(int)
-
-int main(int argc, char *argv[])
-{
- int i, N = 10000000;
- int *array, x;
- clock_t t1, t2;
- if (argc > 1) N = atoi(argv[1]);
- array = (int*)malloc(sizeof(int) * N);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- x = ks_ksmall(int, N, array, 10500);
- t2 = clock();
- fprintf(stderr, "ksmall [%d]: %.3lf\n", x, (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- ks_introsort(int, N, array);
- t2 = clock();
- fprintf(stderr, "introsort [%d]: %.3lf\n", array[10500], (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in introsort!\n");
- exit(1);
- }
- }
-
-#ifndef _ALIGNED_ONLY
- { // test unaligned ksmall
- srand48(11);
- unsigned char *a;
- int *b;
- a = malloc(N * sizeof(int) + 1);
- b = (int*)(a + 1);
- for (i = 0; i < N; ++i) b[i] = (int)lrand48();
- t1 = clock();
- ks_introsort(int, N, b);
- t2 = clock();
- fprintf(stderr, "introsort [%d]: %.3lf (unaligned: 0x%lx) \n", b[10500], (double)(t2-t1)/CLOCKS_PER_SEC, (size_t)b);
- }
-#endif
-
- t1 = clock();
- ks_introsort(int, N, array);
- t2 = clock();
- fprintf(stderr, "introsort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- ks_combsort(int, N, array);
- t2 = clock();
- fprintf(stderr, "combsort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in combsort!\n");
- exit(1);
- }
- }
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- ks_mergesort(int, N, array, 0);
- t2 = clock();
- fprintf(stderr, "mergesort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in mergesort!\n");
- exit(1);
- }
- }
-
- t1 = clock();
- ks_mergesort(int, N, array, 0);
- t2 = clock();
- fprintf(stderr, "mergesort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- ks_heapmake(int, N, array);
- ks_heapsort(int, N, array);
- t2 = clock();
- fprintf(stderr, "heapsort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in heapsort!\n");
- exit(1);
- }
- }
-
- free(array);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/ksort_test.cc b/debian/vendor-h2o/deps/klib/test/ksort_test.cc
deleted file mode 100644
index 8950d80..0000000
--- a/debian/vendor-h2o/deps/klib/test/ksort_test.cc
+++ /dev/null
@@ -1,997 +0,0 @@
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-#include <time.h>
-#include <algorithm>
-
-#include "ksort.h"
-KSORT_INIT_GENERIC(int)
-
-using namespace std;
-
-/**********************************
- * BEGIN OF PAUL'S IMPLEMENTATION *
- **********************************/
-
-/* Attractive Chaos: I have added inline where necessary. */
-
-/*
-Copyright (c) 2004 Paul Hsieh
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
- Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
-
- Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
-
- Neither the name of sorttest nor the names of its contributors may be
- used to endorse or promote products derived from this software without
- specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGE.
-*/
-
-/*
-
-Recommended flags:
-------------------
-
-Intel C/C++:
-icl /O2 /G6 /Qaxi /Qxi /Qip sorttest.c
-
-WATCOM C/C++:
-wcl386 /otexan /6r sorttest.c
-
-GCC:
-gcc -O3 -mcpu=athlon-xp -march=athlon-xp sorttest.c
-
-MSVC:
-cl /O2 /Ot /Og /G6 sorttest.c
-
-*/
-
-static inline void sort2 (int * numbers) {
-int tmp;
-
- if (numbers[0] <= numbers[1]) return;
- tmp = numbers[0];
- numbers[0] = numbers[1];
- numbers[1] = tmp;
-}
-
-static inline void sort3 (int * numbers) {
-int tmp;
-
- if (numbers[0] <= numbers[1]) {
- if (numbers[1] <= numbers[2]) return;
- if (numbers[2] <= numbers[0]) {
- tmp = numbers[0];
- numbers[0] = numbers[2];
- numbers[2] = numbers[1];
- numbers[1] = tmp;
- return;
- }
- tmp = numbers[1];
- } else {
- tmp = numbers[0];
- if (numbers[0] <= numbers[2]) {
- numbers[0] = numbers[1];
- numbers[1] = tmp;
- return;
- }
- if (numbers[2] <= numbers[1]) {
- numbers[0] = numbers[2];
- numbers[2] = tmp;
- return;
- }
- numbers[0] = numbers[1];
- }
- numbers[1] = numbers[2];
- numbers[2] = tmp;
-}
-
-static inline void sort4 (int * num) {
-int tmp;
- if (num[0] < num[1]) {
- if (num[1] < num[2]) {
- if (num[1] < num[3]) {
- if (num[2] >= num[3]) {
- tmp = num[2];
- num[2] = num[3];
- num[3] = tmp;
- }
- } else {
- tmp = num[1];
- if (num[0] < num[3]) {
- num[1] = num[3];
- } else {
- num[1] = num[0];
- num[0] = num[3];
- }
- num[3] = num[2];
- num[2] = tmp;
- }
- } else {
- if (num[0] < num[2]) {
- if (num[2] < num[3]) {
- if (num[1] < num[3]) {
- tmp = num[1];
- } else {
- tmp = num[3];
- num[3] = num[1];
- }
- num[1] = num[2];
- num[2] = tmp;
- } else {
- if (num[0] < num[3]) {
- tmp = num[3];
- } else {
- tmp = num[0];
- num[0] = num[3];
- }
- num[3] = num[1];
- num[1] = tmp;
- }
- } else {
- if (num[0] < num[3]) {
- tmp = num[0];
- num[0] = num[2];
- if (num[1] < num[3]) {
- num[2] = num[1];
- } else {
- num[2] = num[3];
- num[3] = num[1];
- }
- num[1] = tmp;
- } else {
- if (num[2] < num[3]) {
- tmp = num[0];
- num[0] = num[2];
- num[2] = tmp;
- tmp = num[1];
- num[1] = num[3];
- } else {
- tmp = num[1];
- num[1] = num[2];
- num[2] = num[0];
- num[0] = num[3];
- }
- num[3] = tmp;
- }
- }
- }
- } else {
- tmp = num[0];
- if (tmp < num[2]) {
- if (tmp < num[3]) {
- num[0] = num[1];
- num[1] = tmp;
- if (num[2] >= num[3]) {
- tmp = num[2];
- num[2] = num[3];
- num[3] = tmp;
- }
- } else {
- if (num[1] < num[3]) {
- num[0] = num[1];
- num[1] = num[3];
- } else {
- num[0] = num[3];
- }
- num[3] = num[2];
- num[2] = tmp;
- }
- } else {
- if (num[1] < num[2]) {
- if (num[2] < num[3]) {
- num[0] = num[1];
- num[1] = num[2];
- if (tmp < num[3]) {
- num[2] = tmp;
- } else {
- num[2] = num[3];
- num[3] = tmp;
- }
- } else {
- if (num[1] < num[3]) {
- num[0] = num[1];
- num[1] = num[3];
- } else {
- num[0] = num[3];
- }
- num[3] = tmp;
- }
- } else {
- if (num[1] < num[3]) {
- num[0] = num[2];
- if (tmp < num[3]) {
- num[2] = tmp;
- } else {
- num[2] = num[3];
- num[3] = tmp;
- }
- } else {
- if (num[2] < num[3]) {
- num[0] = num[2];
- num[2] = num[1];
- num[1] = num[3];
- num[3] = tmp;
- } else {
- num[0] = num[3];
- num[3] = tmp;
- tmp = num[1];
- num[1] = num[2];
- num[2] = tmp;
- }
- }
- }
- }
- }
-}
-
-static inline void sortAlt2 (int * numbers, int * altNumbers) {
- if (numbers[0] <= numbers[1]) {
- altNumbers[0] = numbers[0];
- altNumbers[1] = numbers[1];
- } else {
- altNumbers[0] = numbers[1];
- altNumbers[1] = numbers[0];
- }
-}
-
-static inline void sortAlt3 (int * numbers, int * altNumbers) {
- if (numbers[0] <= numbers[1]) {
- if (numbers[1] <= numbers[2]) {
- altNumbers[0] = numbers[0];
- altNumbers[1] = numbers[1];
- altNumbers[2] = numbers[2];
- } else if (numbers[2] <= numbers[0]) {
- altNumbers[0] = numbers[2];
- altNumbers[1] = numbers[0];
- altNumbers[2] = numbers[1];
- } else {
- altNumbers[0] = numbers[0];
- altNumbers[1] = numbers[2];
- altNumbers[2] = numbers[1];
- }
- } else {
- if (numbers[0] <= numbers[2]) {
- altNumbers[0] = numbers[1];
- altNumbers[1] = numbers[0];
- altNumbers[2] = numbers[2];
- } else if (numbers[2] <= numbers[1]) {
- altNumbers[0] = numbers[2];
- altNumbers[1] = numbers[1];
- altNumbers[2] = numbers[0];
- } else {
- altNumbers[0] = numbers[1];
- altNumbers[1] = numbers[2];
- altNumbers[2] = numbers[0];
- }
- }
-}
-
-/*
- * Insert Sort
- */
-
-inline void insertSort (int numbers[], int qty) {
-int i, j, idx, q4;
-int tmp;
-
- if (qty <= 4) {
- if (qty == 4) sort4 (numbers);
- else if (qty == 3) sort3 (numbers);
- else if (qty == 2) sort2 (numbers);
- return;
- }
-
- q4 = qty - 4;
-
- for (i=0; i < q4; i++) {
- idx = i;
- for (j=i+1; j < qty; j++) {
- if (numbers[j] < numbers[idx]) idx = j;
- }
- if (idx != i) {
- tmp = numbers[idx];
- numbers[idx] = numbers[i];
- numbers[i] = tmp;
- }
- }
-
- sort4 (numbers + q4);
-}
-
-/*
- * Heap Sort
- */
-
-/* Assure the heap property for entries from top to last */
-static void siftDown (int numbers[], int top, int last) {
-int tmp = numbers[top];
-int maxIdx = top;
-
- while (last >= (maxIdx += maxIdx)) {
-
- /* This is where the comparison occurrs and where a sufficiently
- good compiler can use a computed conditional result rather
- than using control logic. */
- if (maxIdx != last && numbers[maxIdx] < numbers[maxIdx + 1]) maxIdx++;
-
- if (tmp >= numbers[maxIdx]) break;
- numbers[top] = numbers[maxIdx];
- top = maxIdx;
- }
- numbers[top] = tmp;
-}
-
-/* Peel off the top siftDown operation since its parameters are trivial to
- fill in directly (and this saves us some moves.) */
-static void siftDown0 (int numbers[], int last) {
-int tmp;
-
- if (numbers[0] < numbers[1]) {
- tmp = numbers[1];
- numbers[1] = numbers[0];
- siftDown (numbers, 1, last);
- } else {
- tmp = numbers[0];
- }
- numbers[0] = numbers[last];
- numbers[last] = tmp;
-}
-
-void heapSort (int numbers[], int qty) {
-int i;
-
- if (qty <= 4) {
- if (qty == 4) sort4 (numbers);
- else if (qty == 3) sort3 (numbers);
- else if (qty == 2) sort2 (numbers);
- return;
- }
-
- i = qty / 2;
- /* Enforce the heap property for each position in the tree */
- for ( qty--; i > 0; i--) siftDown (numbers, i, qty);
- for (i = qty; i > 0; i--) siftDown0 (numbers, i);
-}
-
-/*
- * Quick Sort
- */
-
-static int medianOf3 (int * numbers, int i, int j) {
-int tmp;
-
- if (numbers[0] <= numbers[i]) {
- if (numbers[j] <= numbers[0]) return numbers[0]; /* j 0 i */
- if (numbers[i] <= numbers[j]) j = i; /* 0 i j */
- /* 0 j i */
- } else {
- if (numbers[0] <= numbers[j]) return numbers[0]; /* i 0 j */
- if (numbers[j] <= numbers[i]) j = i; /* j i 0 */
- /* i j 0 */
- }
- tmp = numbers[j];
- numbers[j] = numbers[0];
- numbers[0] = tmp;
- return tmp;
-}
-
-static void quickSortRecurse (int * numbers, int left, int right) {
-int pivot, lTmp, rTmp;
-
- qsrStart:;
-
-#if defined(__GNUC__)
- if (right <= left + 8) {
- insertSort (numbers + left, right - left + 1);
- return;
- }
-#else
- if (right <= left + 3) {
- if (right == left + 1) {
- sort2 (numbers + left);
- } else if (right == left + 2) {
- sort3 (numbers + left);
- } else if (right == left + 3) {
- sort4 (numbers + left);
- }
- return;
- }
-#endif
-
- lTmp = left;
- rTmp = right;
-
- pivot = medianOf3 (numbers + left, (right-left) >> 1, right-1-left);
-
- goto QStart;
- while (1) {
- do {
- right--;
- if (left >= right) goto QEnd;
- QStart:;
- } while (numbers[right] > pivot);
- numbers[left] = numbers[right];
- do {
- left++;
- if (left >= right) {
- left = right;
- goto QEnd;
- }
- } while (numbers[ left] < pivot);
- numbers[right] = numbers[left];
- }
- QEnd:;
- numbers[left] = pivot;
-
- /* Only recurse the smaller partition */
-
- if (left-1 - lTmp <= rTmp - left - 1) {
- if (lTmp < left) quickSortRecurse (numbers, lTmp, left-1);
-
- /* Set up for larger partition */
- left++;
- right = rTmp;
- } else {
- if (rTmp > left) quickSortRecurse (numbers, left+1, rTmp);
-
- /* Set up for larger partition */
- right = left - 1;
- left = lTmp;
- }
-
- /* Rerun with larger partition (recursion not required.) */
- goto qsrStart;
-}
-
-void quickSort (int numbers[], int qty) {
- if (qty < 2) return;
- quickSortRecurse (numbers, 0, qty - 1);
-}
-
-/*
- * Merge Sort
- */
-
-static void mergesortInPlace (int * numbers, int * altNumbers, int qty);
-
-/* Perform mergesort, but store results in altNumbers */
-
-static void mergesortExchange (int * numbers, int * altNumbers, int qty) {
-int half, i0, i1, i;
-
- if (qty == 2) {
- sortAlt2 (numbers, altNumbers);
- return;
- }
- if (qty == 3) {
- sortAlt3 (numbers, altNumbers);
- return;
- }
-
- half = (qty + 1)/2;
-
- mergesortInPlace (numbers, altNumbers, half);
- mergesortInPlace (numbers + half, altNumbers, qty - half);
-
- i0 = 0; i1 = half;
-
- for (i=0; i < qty; i++) {
- if (i1 >= qty || (i0 < half && numbers[i0] < numbers[i1])) {
- altNumbers[i] = numbers[i0];
- i0++;
- } else {
- altNumbers[i] = numbers[i1];
- i1++;
- }
- }
-}
-
-/* Perform mergesort and store results in numbers */
-
-static void mergesortInPlace (int * numbers, int * altNumbers, int qty) {
-int half, i0, i1, i;
-
-#if 0
- if (qty == 2) {
- sort2 (numbers);
- return;
- }
- if (qty == 3) {
- sort3 (numbers);
- return;
- }
- if (qty == 4) {
- sort4 (numbers);
- return;
- }
-#else
- if (qty <= 12) {
- insertSort (numbers, qty);
- return;
- }
-#endif
-
- half = (qty + 1)/2;
-
- mergesortExchange (numbers, altNumbers, half);
- mergesortExchange (numbers + half, altNumbers + half, qty - half);
-
- i0 = 0; i1 = half;
-
- for (i=0; i < qty; i++) {
- if (i1 >= qty || (i0 < half && altNumbers[i0] < altNumbers[i1])) {
- numbers[i] = altNumbers[i0];
- i0++;
- } else {
- numbers[i] = altNumbers[i1];
- i1++;
- }
- }
-}
-
-#include <stdlib.h>
-
-void mergeSort (int numbers[], int qty) {
-int * tmpArray;
-
- if (qty <= 12) {
- insertSort (numbers, qty);
- return;
- }
-
- tmpArray = (int *) malloc (qty * sizeof (int));
- mergesortInPlace (numbers, tmpArray, qty);
- free (tmpArray);
-}
-
-/********************************
- * END OF PAUL'S IMPLEMENTATION *
- ********************************/
-
-/*************************************************
- *** Implementation 1: faster on sorted arrays ***
- *************************************************/
-
-#define rstype_t unsigned
-#define rskey(x) (x)
-
-#define RS_MIN_SIZE 64
-
-typedef struct {
- rstype_t *b, *e;
-} rsbucket_t;
-
-void rs_sort(rstype_t *beg, rstype_t *end, int n_bits, int s)
-{
- rstype_t *i;
- int size = 1<<n_bits, m = size - 1;
- rsbucket_t *k, b[size], *be = b + size;
-
- for (k = b; k != be; ++k) k->b = k->e = beg;
- for (i = beg; i != end; ++i) ++b[rskey(*i)>>s&m].e;
- for (k = b + 1; k != be; ++k)
- k->e += (k-1)->e - beg, k->b = (k-1)->e;
- for (k = b; k != be;) {
- if (k->b != k->e) {
- rsbucket_t *l;
- if ((l = b + (rskey(*k->b)>>s&m)) != k) {
- rstype_t tmp = *k->b, swap;
- do {
- swap = tmp; tmp = *l->b; *l->b++ = swap;
- l = b + (rskey(tmp)>>s&m);
- } while (l != k);
- *k->b++ = tmp;
- } else ++k->b;
- } else ++k;
- }
- for (b->b = beg, k = b + 1; k != be; ++k) k->b = (k-1)->e;
- if (s) {
- s = s > n_bits? s - n_bits : 0;
- for (k = b; k != be; ++k)
- if (k->e - k->b > RS_MIN_SIZE) rs_sort(k->b, k->e, n_bits, s);
- else if (k->e - k->b > 1)
- for (i = k->b + 1; i < k->e; ++i)
- if (rskey(*i) < rskey(*(i - 1))) {
- rstype_t *j, tmp = *i;
- for (j = i; j > k->b && rskey(tmp) < rskey(*(j-1)); --j)
- *j = *(j - 1);
- *j = tmp;
- }
- }
-}
-
-/*************************************************
- *** Implementation 2: faster on random arrays ***
- *************************************************/
-
-static inline void rs_insertsort(rstype_t *s, rstype_t *t)
-{
- rstype_t *i;
- for (i = s + 1; i < t; ++i) {
- if (rskey(*i) < rskey(*(i - 1))) {
- rstype_t *j, tmp = *i;
- for (j = i; j > s && rskey(tmp) < rskey(*(j-1)); --j)
- *j = *(j - 1);
- *j = tmp;
- }
- }
-}
-/*
-void rs_sort2(rstype_t *beg, rstype_t *end, int n_bits, int s)
-{
- int j, size = 1<<n_bits, m = size - 1;
- unsigned long c[size];
- rstype_t *i, *b[size], *e[size];
-
- for (j = 0; j < size; ++j) c[j] = 0;
- for (i = beg; i != end; ++i) ++c[rskey(*i)>>s&m];
- b[0] = e[0] = beg;
- for (j = 1; j != size; ++j) b[j] = e[j] = b[j - 1] + c[j - 1];
- for (i = beg, j = 0; i != end;) {
- rstype_t tmp = *i, swap;
- int x;
- for (;;) {
- x = rskey(tmp)>>s&m;
- if (e[x] == i) break;
- swap = tmp; tmp = *e[x]; *e[x]++ = swap;
- }
- *i++ = tmp;
- ++e[x];
- while (j != size && i >= b[j]) ++j;
- while (j != size && e[j-1] == b[j]) ++j;
- if (i < e[j-1]) i = e[j-1];
- }
- if (s) {
- s = s > n_bits? s - n_bits : 0;
- for (j = 0; j < size; ++j) {
- if (c[j] >= RS_MIN_SIZE) rs_sort2(b[j], e[j], n_bits, s);
- else if (c[j] >= 2) rs_insertsort(b[j], e[j]);
- }
- }
-}
-*/
-void radix_sort(unsigned *array, int offset, int end, int shift) {
- int x, y, value, temp;
- int last[256] = { 0 }, pointer[256];
-
- for (x=offset; x<end; ++x) {
- ++last[(array[x] >> shift) & 0xFF];
- }
-
- last[0] += offset;
- pointer[0] = offset;
- for (x=1; x<256; ++x) {
- pointer[x] = last[x-1];
- last[x] += last[x-1];
- }
-
- for (x=0; x<256; ++x) {
- while (pointer[x] != last[x]) {
- value = array[pointer[x]];
- y = (value >> shift) & 0xFF;
- while (x != y) {
- temp = array[pointer[y]];
- array[pointer[y]++] = value;
- value = temp;
- y = (value >> shift) & 0xFF;
- }
- array[pointer[x]++] = value;
- }
- }
-
- if (shift > 0) {
- shift -= 8;
- for (x=0; x<256; ++x) {
- temp = x > 0 ? pointer[x] - pointer[x-1] : pointer[0] - offset;
- if (temp > 64) {
- radix_sort(array, pointer[x] - temp, pointer[x], shift);
- } else if (temp > 1) rs_insertsort(array + pointer[x] - temp, array + pointer[x]);
- }
- }
-}
-/*************************
- *** END OF RADIX SORT ***
- *************************/
-
-template< class _Type, unsigned long PowerOfTwoRadix, unsigned long Log2ofPowerOfTwoRadix, long Threshold >
-inline void _RadixSort_Unsigned_PowerOf2Radix_1( _Type* a, long last, _Type bitMask, unsigned long shiftRightAmount )
-{
- const unsigned long numberOfBins = PowerOfTwoRadix;
- unsigned long count[ numberOfBins ];
- for( unsigned long i = 0; i < numberOfBins; i++ )
- count[ i ] = 0;
- for ( long _current = 0; _current <= last; _current++ ) // Scan the array and count the number of times each value appears
- {
- unsigned long digit = (unsigned long)(( a[ _current ] & bitMask ) >> shiftRightAmount ); // extract the digit we are sorting based on
- count[ digit ]++;
- }
- long startOfBin[ numberOfBins ], endOfBin[ numberOfBins ], nextBin;
- startOfBin[ 0 ] = endOfBin[ 0 ] = nextBin = 0;
- for( unsigned long i = 1; i < numberOfBins; i++ )
- startOfBin[ i ] = endOfBin[ i ] = startOfBin[ i - 1 ] + count[ i - 1 ];
- for ( long _current = 0; _current <= last; )
- {
- unsigned long digit;
- _Type tmp = a[ _current ]; // get the compiler to recognize that a register can be used for the loop instead of a[_current] memory location
- while ( true ) {
- digit = (unsigned long)(( tmp & bitMask ) >> shiftRightAmount ); // extract the digit we are sorting based on
- if ( endOfBin[ digit ] == _current )
- break;
- _Type tmp2;
- //_swap( tmp, a[ endOfBin[ digit ] ] );
- tmp2 = a[endOfBin[digit]]; a[endOfBin[digit]] = tmp; tmp = tmp2;
- endOfBin[ digit ]++;
- }
- a[ _current ] = tmp;
- endOfBin[ digit ]++; // leave the element at its location and grow the bin
- _current++; // advance the current pointer to the next element
- while( _current >= startOfBin[ nextBin ] && nextBin < numberOfBins )
- nextBin++;
- while( endOfBin[ nextBin - 1 ] == startOfBin[ nextBin ] && nextBin < numberOfBins )
- nextBin++;
- if ( _current < endOfBin[ nextBin - 1 ] )
- _current = endOfBin[ nextBin - 1 ];
- }
- bitMask >>= Log2ofPowerOfTwoRadix;
- if ( bitMask != 0 ) // end recursion when all the bits have been processes
- {
- if ( shiftRightAmount >= Log2ofPowerOfTwoRadix ) shiftRightAmount -= Log2ofPowerOfTwoRadix;
- else shiftRightAmount = 0;
- for( unsigned long i = 0; i < numberOfBins; i++ )
- {
- long numberOfElements = endOfBin[ i ] - startOfBin[ i ];
- if ( numberOfElements >= Threshold ) // endOfBin actually points to one beyond the bin
- _RadixSort_Unsigned_PowerOf2Radix_1< _Type, PowerOfTwoRadix, Log2ofPowerOfTwoRadix, Threshold >( &a[ startOfBin[ i ]], numberOfElements - 1, bitMask, shiftRightAmount );
- else if ( numberOfElements >= 2 )
- rs_insertsort(&a[ startOfBin[ i ]], &a[ endOfBin[ i ]]);
- }
- }
-}
-inline void RadixSortInPlace_HybridUnsigned_Radix256( unsigned* a, unsigned long a_size )
-{
- if ( a_size < 2 ) return;
- unsigned long bitMask = 0xFF000000; // bitMask controls how many bits we process at a time
- unsigned long shiftRightAmount = 24;
- if ( a_size >= 32 )
- _RadixSort_Unsigned_PowerOf2Radix_1<unsigned, 256, 8, 32>(a, a_size - 1, bitMask, shiftRightAmount );
- else
- rs_insertsort(a, a + a_size);
-}
-
-struct intcmp_t {
- inline int operator() (int a, int b) const {
- return a < b? -1 : a > b? 1 : 0;
- }
-};
-
-int compare_int(int a, int b)
-{
- return a < b? -1 : a > b? 1 : 0;
-}
-int compare(const void *a, const void *b)
-{
- return *((int*)a) - *((int*)b);
-}
-
-int main(int argc, char *argv[])
-{
- int i, N = 50000000;
- int *array, *temp;
- clock_t t1, t2;
- if (argc == 1) fprintf(stderr, "Usage: %s [%d]\n", argv[0], N);
- if (argc > 1) N = atoi(argv[1]);
- temp = (int*)malloc(sizeof(int) * N);
- array = (int*)malloc(sizeof(int) * N);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- rs_sort((unsigned*)array, (unsigned*)array + N, 8, 24);
- t2 = clock();
- fprintf(stderr, "radix sort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in radix sort!\n");
- exit(1);
- }
- }
- t1 = clock();
- rs_sort((unsigned*)array, (unsigned*)array + N, 8, 24);
- t2 = clock();
- fprintf(stderr, "radix sort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- RadixSortInPlace_HybridUnsigned_Radix256((unsigned*)array, N);
-// radix_sort((unsigned*)array, 0, N, 24);
- t2 = clock();
- fprintf(stderr, "vd's radix sort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in radix sort!\n");
- exit(1);
- }
- }
- t1 = clock();
- RadixSortInPlace_HybridUnsigned_Radix256((unsigned*)array, N);
-// radix_sort((unsigned*)array, 0, N, 24);
- t2 = clock();
- fprintf(stderr, "vd's radix sort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- sort(array, array+N);
- t2 = clock();
- fprintf(stderr, "STL introsort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- t1 = clock();
- sort(array, array+N);
- t2 = clock();
- fprintf(stderr, "STL introsort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- stable_sort(array, array+N);
- t2 = clock();
- fprintf(stderr, "STL stablesort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- t1 = clock();
- stable_sort(array, array+N);
- t2 = clock();
- fprintf(stderr, "STL stablesort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- make_heap(array, array+N);
- sort_heap(array, array+N);
- t2 = clock();
- fprintf(stderr, "STL heapsort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in heap_sort!\n");
- exit(1);
- }
- }
- t1 = clock();
- make_heap(array, array+N);
- sort_heap(array, array+N);
- t2 = clock();
- fprintf(stderr, "STL heapsort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- ks_combsort(int, N, array);
- t2 = clock();
- fprintf(stderr, "combsort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in combsort!\n");
- exit(1);
- }
- }
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- qsort(array, N, sizeof(int), compare);
- t2 = clock();
- fprintf(stderr, "libc qsort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- ks_introsort(int, N, array);
- t2 = clock();
- fprintf(stderr, "my introsort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in intro_sort!\n");
- exit(1);
- }
- }
- t1 = clock();
- ks_introsort(int, N, array);
- t2 = clock();
- fprintf(stderr, "introsort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- ks_mergesort(int, N, array, 0);
- t2 = clock();
- fprintf(stderr, "iterative mergesort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in merge_sort!\n");
- exit(1);
- }
- }
- t1 = clock();
- ks_mergesort(int, N, array, 0);
- t2 = clock();
- fprintf(stderr, "iterative mergesort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- ks_heapmake(int, N, array);
- ks_heapsort(int, N, array);
- t2 = clock();
- fprintf(stderr, "my heapsort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in heap_sort!\n");
- exit(1);
- }
- }
- t1 = clock();
- ks_heapmake(int, N, array);
- ks_heapsort(int, N, array);
- t2 = clock();
- fprintf(stderr, "heapsort (sorted): %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- heapSort(array, N);
- t2 = clock();
- fprintf(stderr, "Paul's heapsort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in intro_sort!\n");
- exit(1);
- }
- }
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- quickSort(array, N);
- t2 = clock();
- fprintf(stderr, "Paul's quicksort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in intro_sort!\n");
- exit(1);
- }
- }
-
- srand48(11);
- for (i = 0; i < N; ++i) array[i] = (int)lrand48();
- t1 = clock();
- mergeSort(array, N);
- t2 = clock();
- fprintf(stderr, "Paul's mergesort: %.3lf\n", (double)(t2-t1)/CLOCKS_PER_SEC);
- for (i = 0; i < N-1; ++i) {
- if (array[i] > array[i+1]) {
- fprintf(stderr, "Bug in intro_sort!\n");
- exit(1);
- }
- }
-
- free(array); free(temp);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kstring_bench.c b/debian/vendor-h2o/deps/klib/test/kstring_bench.c
deleted file mode 100644
index 82598e8..0000000
--- a/debian/vendor-h2o/deps/klib/test/kstring_bench.c
+++ /dev/null
@@ -1,51 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <time.h>
-#include "kstring.h"
-
-#define N 10000000
-
-int main()
-{
- int i;
- clock_t t;
- kstring_t s, s2;
- srand48(11);
- s.l = s.m = 0; s.s = 0;
- t = clock();
- for (i = 0; i < N; ++i) {
- int x = lrand48();
- s.l = 0;
- kputw(x, &s);
- }
- fprintf(stderr, "kputw: %lf\n", (double)(clock() - t) / CLOCKS_PER_SEC);
- srand48(11);
- t = clock();
- for (i = 0; i < N; ++i) {
- int x = lrand48();
- s.l = 0;
- ksprintf(&s, "%d", x);
- }
- fprintf(stderr, "ksprintf: %lf\n", (double)(clock() - t) / CLOCKS_PER_SEC);
-
- srand48(11);
- s2.l = s2.m = 0; s2.s = 0;
- t = clock();
- for (i = 0; i < N; ++i) {
- int x = lrand48();
- s2.l = s.l = 0;
- kputw(x, &s2);
- kputs(s2.s, &s);
- }
- fprintf(stderr, "kputw+kputs: %lf\n", (double)(clock() - t) / CLOCKS_PER_SEC);
- srand48(11);
- t = clock();
- for (i = 0; i < N; ++i) {
- int x = lrand48();
- s2.l = s.l = 0;
- kputw(x, &s2);
- ksprintf(&s, "%s", s2.s);
- }
- fprintf(stderr, "kputw+ksprintf: %lf\n", (double)(clock() - t) / CLOCKS_PER_SEC);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kstring_bench2.c b/debian/vendor-h2o/deps/klib/test/kstring_bench2.c
deleted file mode 100644
index b7707a8..0000000
--- a/debian/vendor-h2o/deps/klib/test/kstring_bench2.c
+++ /dev/null
@@ -1,131 +0,0 @@
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <time.h>
-#include "kstring.h"
-
-#ifdef __APPLE__
-#define HAVE_STRNSTR
-#endif
-
-#ifdef __linux__
-#define HAVE_MEMMEM
-#endif
-
-static int str_len = 1024*1024*128;
-static int pat_len = 30;
-static int alphabet = 2;
-static int repeat = 50;
-
-char *gen_data(int len, int a)
-{
- char *data;
- int i;
- long x;
- srand48(11);
- data = malloc(len);
- for (i = 0; i < len; ++i)
- data[i] = (int)(a * drand48()) + '!';
- data[str_len - 1] = 0;
- return data;
-}
-// http://srcvault.scali.eu.org/cgi-bin/Syntax/c/BoyerMoore.c
-char *BoyerMoore( unsigned char *data, unsigned int dataLength, unsigned char *string, unsigned int strLength )
-{
- unsigned int skipTable[256], i;
- unsigned char *search;
- register unsigned char lastChar;
-
- if (strLength == 0)
- return NULL;
-
- for (i = 0; i < 256; i++)
- skipTable[i] = strLength;
- search = string;
- i = --strLength;
- do {
- skipTable[*search++] = i;
- } while (i--);
- lastChar = *--search;
- search = data + strLength;
- dataLength -= strLength+(strLength-1);
- while ((int)dataLength > 0 ) {
- unsigned int skip;
- skip = skipTable[*search];
- search += skip;
- dataLength -= skip;
- skip = skipTable[*search];
- search += skip;
- dataLength -= skip;
- skip = skipTable[*search];
- if (*search != lastChar) {
- search += skip;
- dataLength -= skip;
- continue;
- }
- i = strLength;
- do {
- if (i-- == 0) return search;
- } while (*--search == string[i]);
- search += (strLength - i + 1);
- dataLength--;
- }
- return NULL;
-}
-
-int main()
-{
- char *data;
- int i;
- clock_t t;
- t = clock();
- data = gen_data(str_len, alphabet);
- fprintf(stderr, "Generate data in %.3f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- {
- t = clock(); srand48(1331);
- for (i = 0; i < repeat; ++i) {
- int y = lrand48() % (str_len - pat_len);
- char *ret;
- ret = kmemmem(data, str_len, data + y, pat_len, 0);
-// printf("%d, %d\n", (int)(ret - data), y);
- }
- fprintf(stderr, "Search patterns in %.3f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
- if (1) {
- t = clock(); srand48(1331);
- for (i = 0; i < repeat; ++i) {
- int y = lrand48() % (str_len - pat_len);
- char *ret;
- ret = BoyerMoore(data, str_len, data + y, pat_len);
-// printf("%d, %d\n", (int)(ret - data), y);
- }
- fprintf(stderr, "Search patterns in %.3f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
-#ifdef HAVE_STRNSTR
- if (1) {
- char *tmp;
- t = clock(); srand48(1331);
- tmp = calloc(pat_len+1, 1);
- for (i = 0; i < repeat; ++i) {
- int y = lrand48() % (str_len - pat_len);
- char *ret;
- memcpy(tmp, data + y, pat_len);
- ret = strnstr(data, tmp, str_len);
- }
- fprintf(stderr, "Search patterns in %.3f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
-#endif
-#ifdef HAVE_MEMMEM
- if (1) {
- t = clock(); srand48(1331);
- for (i = 0; i < repeat; ++i) {
- int y = lrand48() % (str_len - pat_len);
- char *ret;
- ret = memmem(data, str_len, data + y, pat_len);
-// printf("%d, %d\n", (int)(ret - data), y);
- }
- fprintf(stderr, "Search patterns in %.3f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
-#endif
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kstring_test.c b/debian/vendor-h2o/deps/klib/test/kstring_test.c
deleted file mode 100644
index 76f9532..0000000
--- a/debian/vendor-h2o/deps/klib/test/kstring_test.c
+++ /dev/null
@@ -1,76 +0,0 @@
-#include <limits.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "kstring.h"
-
-int nfail = 0;
-
-void check(const char *what, const kstring_t *ks, const char *correct)
-{
- if (ks->l != strlen(correct) || strcmp(ks->s, correct) != 0) {
- fprintf(stderr, "%s produced \"%.*s\" (\"%s\" is correct)\tFAIL\n", what, (int)(ks->l), ks->s, correct);
- nfail++;
- }
-}
-
-void test_kputw(kstring_t *ks, int n)
-{
- char buf[16];
-
- ks->l = 0;
- kputw(n, ks);
-
- sprintf(buf, "%d", n);
- check("kputw()", ks, buf);
-}
-
-void test_kputl(kstring_t *ks, long n)
-{
- char buf[24];
-
- ks->l = 0;
- kputl(n, ks);
-
- sprintf(buf, "%ld", n);
- check("kputl()", ks, buf);
-}
-
-int main()
-{
- kstring_t ks;
-
- ks.l = ks.m = 0;
- ks.s = NULL;
-
- test_kputw(&ks, 0);
- test_kputw(&ks, 1);
- test_kputw(&ks, 37);
- test_kputw(&ks, 12345);
- test_kputw(&ks, -12345);
- test_kputw(&ks, INT_MAX);
- test_kputw(&ks, -INT_MAX);
- test_kputw(&ks, INT_MIN);
-
- test_kputl(&ks, 0);
- test_kputl(&ks, 1);
- test_kputl(&ks, 37);
- test_kputl(&ks, 12345);
- test_kputl(&ks, -12345);
- test_kputl(&ks, INT_MAX);
- test_kputl(&ks, -INT_MAX);
- test_kputl(&ks, INT_MIN);
- test_kputl(&ks, LONG_MAX);
- test_kputl(&ks, -LONG_MAX);
- test_kputl(&ks, LONG_MIN);
-
- free(ks.s);
-
- if (nfail > 0) {
- fprintf(stderr, "Total failures: %d\n", nfail);
- return EXIT_FAILURE;
- }
-
- return EXIT_SUCCESS;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kthread_test.c b/debian/vendor-h2o/deps/klib/test/kthread_test.c
deleted file mode 100644
index 1b67ed4..0000000
--- a/debian/vendor-h2o/deps/klib/test/kthread_test.c
+++ /dev/null
@@ -1,69 +0,0 @@
-#include <stdio.h>
-#include <assert.h>
-#include <stdlib.h>
-#include <pthread.h>
-#if HAVE_CILK
-#include <cilk/cilk.h>
-#include <cilk/cilk_api.h>
-#endif
-
-typedef struct {
- int max_iter, w, h;
- double xmin, xmax, ymin, ymax;
- int *k;
-} global_t;
-
-static void compute(void *_g, int i, int tid)
-{
- global_t *g = (global_t*)_g;
- double x, x0 = g->xmin + (g->xmax - g->xmin) * (i%g->w) / g->w;
- double y, y0 = g->ymin + (g->ymax - g->ymin) * (i/g->w) / g->h;
- int k;
-
- assert(g->k[i] < 0);
- x = x0, y = y0;
- for (k = 0; k < g->max_iter; ++k) {
- double z = x * y;
- x *= x; y *= y;
- if (x + y >= 4) break;
- x = x - y + x0;
- y = z + z + y0;
- }
- g->k[i] = k;
-}
-
-void kt_for(int n_threads, int n_items, void (*func)(void*,int,int), void *data);
-
-int main(int argc, char *argv[])
-{
- int i, tmp, tot, type = 0, n_threads = 2;
- global_t global = { 10240*100, 800, 600, -2., -1.2, -1.2, 1.2, 0 };
-// global_t global = { 10240*1, 8, 6, -2., -1.2, -1.2, 1.2, 0 };
-
- if (argc > 1) {
- type = argv[1][0] == 'o'? 2 : argv[1][0] == 'c'? 3 : argv[1][0] == 'n'? 1 : 0;
- if (argv[1][0] >= '0' && argv[1][0] <= '9')
- n_threads = atoi(argv[1]);
- } else {
- fprintf(stderr, "Usage: ./a.out [openmp | cilk | #threads]\n");
- }
- tot = global.w * global.h;
- global.k = calloc(tot, sizeof(int));
- for (i = 0; i < tot; ++i) global.k[i] = -1;
- if (type == 0) {
- kt_for(n_threads, tot, compute, &global);
- } else if (type == 2) {
- #pragma omp parallel for
- for (i = 0; i < tot; ++i)
- compute(&global, i, 0);
- } else if (type == 3) {
- #if HAVE_CILK
- cilk_for (i = 0; i < tot; ++i)
- compute(&global, i, 0);
- #endif
- }
- for (i = tmp = 0; i < tot; ++i) tmp += (global.k[i] < 0);
- free(global.k);
- assert(tmp == 0);
- return 0;
-}
diff --git a/debian/vendor-h2o/deps/klib/test/kvec_test.cc b/debian/vendor-h2o/deps/klib/test/kvec_test.cc
deleted file mode 100644
index 1015574..0000000
--- a/debian/vendor-h2o/deps/klib/test/kvec_test.cc
+++ /dev/null
@@ -1,69 +0,0 @@
-#include <vector>
-#include <time.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include "kvec.h"
-
-int main()
-{
- int M = 10, N = 20000000, i, j;
- clock_t t;
- t = clock();
- for (i = 0; i < M; ++i) {
- int *array = (int*)malloc(N * sizeof(int));
- for (j = 0; j < N; ++j) array[j] = j;
- free(array);
- }
- printf("C array, preallocated: %.3f sec\n",
- (float)(clock() - t) / CLOCKS_PER_SEC);
- t = clock();
- for (i = 0; i < M; ++i) {
- int *array = 0, max = 0;
- for (j = 0; j < N; ++j) {
- if (j == max) {
- max = !max? 1 : max << 1;
- array = (int*)realloc(array, sizeof(int)*max);
- }
- array[j] = j;
- }
- free(array);
- }
- printf("C array, dynamic: %.3f sec\n",
- (float)(clock() - t) / CLOCKS_PER_SEC);
- t = clock();
- for (i = 0; i < M; ++i) {
- kvec_t(int) array;
- kv_init(array);
- kv_resize(int, array, N);
- for (j = 0; j < N; ++j) kv_a(int, array, j) = j;
- kv_destroy(array);
- }
- printf("C vector, dynamic(kv_a): %.3f sec\n",
- (float)(clock() - t) / CLOCKS_PER_SEC);
- t = clock();
- for (i = 0; i < M; ++i) {
- kvec_t(int) array;
- kv_init(array);
- for (j = 0; j < N; ++j)
- kv_push(int, array, j);
- kv_destroy(array);
- }
- printf("C vector, dynamic(kv_push): %.3f sec\n",
- (float)(clock() - t) / CLOCKS_PER_SEC);
- t = clock();
- for (i = 0; i < M; ++i) {
- std::vector<int> array;
- array.reserve(N);
- for (j = 0; j < N; ++j) array[j] = j;
- }
- printf("C++ vector, preallocated: %.3f sec\n",
- (float)(clock() - t) / CLOCKS_PER_SEC);
- t = clock();
- for (i = 0; i < M; ++i) {
- std::vector<int> array;
- for (j = 0; j < N; ++j) array.push_back(j);
- }
- printf("C++ vector, dynamic: %.3f sec\n",
- (float)(clock() - t) / CLOCKS_PER_SEC);
- return 0;
-}