0

Upgrade versions of vendored libs

This commit is contained in:
eleksir
2025-04-06 15:38:36 +03:00
parent 484bfa9ba0
commit 24507ed6b4
144 changed files with 4495 additions and 2316 deletions

View File

@@ -22,8 +22,17 @@
/*-*************************************
* Dependencies
***************************************/
/* qsort_r is an extension. */
#if defined(__linux) || defined(__linux__) || defined(linux) || defined(__gnu_linux__) || \
defined(__CYGWIN__) || defined(__MSYS__)
#if !defined(_GNU_SOURCE) && !defined(__ANDROID__) /* NDK doesn't ship qsort_r(). */
#define _GNU_SOURCE
#endif
#endif
#include <stdio.h> /* fprintf */
#include <stdlib.h> /* malloc, free, qsort */
#include <stdlib.h> /* malloc, free, qsort_r */
#include <string.h> /* memset */
#include <time.h> /* clock */
@@ -233,8 +242,10 @@ typedef struct {
unsigned d;
} COVER_ctx_t;
/* We need a global context for qsort... */
#if !defined(_GNU_SOURCE) && !defined(__APPLE__) && !defined(_MSC_VER)
/* C90 only offers qsort() that needs a global context. */
static COVER_ctx_t *g_coverCtx = NULL;
#endif
/*-*************************************
* Helper functions
@@ -277,11 +288,15 @@ static int COVER_cmp8(COVER_ctx_t *ctx, const void *lp, const void *rp) {
/**
* Same as COVER_cmp() except ties are broken by pointer value
* NOTE: g_coverCtx must be set to call this function. A global is required because
* qsort doesn't take an opaque pointer.
*/
static int WIN_CDECL COVER_strict_cmp(const void *lp, const void *rp) {
int result = COVER_cmp(g_coverCtx, lp, rp);
#if (defined(_WIN32) && defined(_MSC_VER)) || defined(__APPLE__)
static int WIN_CDECL COVER_strict_cmp(void* g_coverCtx, const void* lp, const void* rp) {
#elif defined(_GNU_SOURCE)
static int COVER_strict_cmp(const void *lp, const void *rp, void *g_coverCtx) {
#else /* C90 fallback.*/
static int COVER_strict_cmp(const void *lp, const void *rp) {
#endif
int result = COVER_cmp((COVER_ctx_t*)g_coverCtx, lp, rp);
if (result == 0) {
result = lp < rp ? -1 : 1;
}
@@ -290,14 +305,50 @@ static int WIN_CDECL COVER_strict_cmp(const void *lp, const void *rp) {
/**
* Faster version for d <= 8.
*/
static int WIN_CDECL COVER_strict_cmp8(const void *lp, const void *rp) {
int result = COVER_cmp8(g_coverCtx, lp, rp);
#if (defined(_WIN32) && defined(_MSC_VER)) || defined(__APPLE__)
static int WIN_CDECL COVER_strict_cmp8(void* g_coverCtx, const void* lp, const void* rp) {
#elif defined(_GNU_SOURCE)
static int COVER_strict_cmp8(const void *lp, const void *rp, void *g_coverCtx) {
#else /* C90 fallback.*/
static int COVER_strict_cmp8(const void *lp, const void *rp) {
#endif
int result = COVER_cmp8((COVER_ctx_t*)g_coverCtx, lp, rp);
if (result == 0) {
result = lp < rp ? -1 : 1;
}
return result;
}
/**
* Abstract away divergence of qsort_r() parameters.
* Hopefully when C11 become the norm, we will be able
* to clean it up.
*/
static void stableSort(COVER_ctx_t *ctx) {
#if defined(__APPLE__)
qsort_r(ctx->suffix, ctx->suffixSize, sizeof(U32),
ctx,
(ctx->d <= 8 ? &COVER_strict_cmp8 : &COVER_strict_cmp));
#elif defined(_GNU_SOURCE)
qsort_r(ctx->suffix, ctx->suffixSize, sizeof(U32),
(ctx->d <= 8 ? &COVER_strict_cmp8 : &COVER_strict_cmp),
ctx);
#elif defined(_WIN32) && defined(_MSC_VER)
qsort_s(ctx->suffix, ctx->suffixSize, sizeof(U32),
(ctx->d <= 8 ? &COVER_strict_cmp8 : &COVER_strict_cmp),
ctx);
#elif defined(__OpenBSD__)
g_coverCtx = ctx;
mergesort(ctx->suffix, ctx->suffixSize, sizeof(U32),
(ctx->d <= 8 ? &COVER_strict_cmp8 : &COVER_strict_cmp));
#else /* C90 fallback.*/
g_coverCtx = ctx;
/* TODO(cavalcanti): implement a reentrant qsort() when is not available. */
qsort(ctx->suffix, ctx->suffixSize, sizeof(U32),
(ctx->d <= 8 ? &COVER_strict_cmp8 : &COVER_strict_cmp));
#endif
}
/**
* Returns the first pointer in [first, last) whose element does not compare
* less than value. If no such element exists it returns last.
@@ -621,17 +672,7 @@ static size_t COVER_ctx_init(COVER_ctx_t *ctx, const void *samplesBuffer,
for (i = 0; i < ctx->suffixSize; ++i) {
ctx->suffix[i] = i;
}
/* qsort doesn't take an opaque pointer, so pass as a global.
* On OpenBSD qsort() is not guaranteed to be stable, their mergesort() is.
*/
g_coverCtx = ctx;
#if defined(__OpenBSD__)
mergesort(ctx->suffix, ctx->suffixSize, sizeof(U32),
(ctx->d <= 8 ? &COVER_strict_cmp8 : &COVER_strict_cmp));
#else
qsort(ctx->suffix, ctx->suffixSize, sizeof(U32),
(ctx->d <= 8 ? &COVER_strict_cmp8 : &COVER_strict_cmp));
#endif
stableSort(ctx);
}
DISPLAYLEVEL(2, "Computing frequencies\n");
/* For each dmer group (group of positions with the same first d bytes):