fast-bwa/utils.h

/* The MIT License

   Copyright (c) 2018-     Dana-Farber Cancer Institute
                 2009-2018 Broad Institute, Inc.
                 2008-2009 Genome Research Ltd. (GRL)

   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 LH3_UTILS_H
#define LH3_UTILS_H

#include <stdint.h>
#include <stdio.h>
#include <zlib.h>

// for debug and test

//#define DEBUG_OUTPUT // 打开gfp1-4文件，并记录debug信息
//#define COUNT_SEED_LENGTH // 记录seed匹配数量降低到1时的长度，以及最终扩展的长度
//#define GET_FULL_MATCH_READ // 获取完全匹配的reads
//#define COUNT_CALC_NUM // 统计BSW的剪枝后的计算量和未剪枝前的计算量
// #define GET_DIFFERENT_EXTENSION_LENGTH // 获取不同长度extension的query，target，和其他用于计算的数据
//#define DEBUG_SW_EXTEND // 将bsw的分值输入到debug文件里

////////////////////

#define USE_RDTSC 1

#ifdef SHOW_PERF
extern uint64_t time_process_data, time_read, time_write, time_compute,
			    time_seed_1, time_seed_2, time_seed_3,
			    time_seed_sa, time_seed_chain, time_seed_all,
			    time_bsw, time_bsw_all,
			    time_work_kernel, time_work_sam,
				time_load_idx;
extern uint64_t proc_freq;
#endif

#ifdef SHOW_DATA_PERF
extern int64_t gdat[100];
#endif

#ifdef DEBUG_OUTPUT
extern FILE *gfp1, *gfp2, *gfp3, *gfp4;
extern FILE *gfq[4], *gft[4], *gfi[4];
#endif

#undef MAX
#undef MIN
#define MAX(x, y) ((x) > (y) ? (x) : (y))
#define MIN(x, y) ((x) < (y) ? (x) : (y))

#ifdef __GNUC__
// Tell GCC to validate printf format string and args
#define ATTRIBUTE(list) __attribute__ (list)
#else
#define ATTRIBUTE(list)
#endif

#define err_fatal_simple(msg) _err_fatal_simple(__func__, msg)
#define err_fatal_simple_core(msg) _err_fatal_simple_core(__func__, msg)

#define xopen(fn, mode) err_xopen_core(__func__, fn, mode)
#define xreopen(fn, mode, fp) err_xreopen_core(__func__, fn, mode, fp)
#define xzopen(fn, mode) err_xzopen_core(__func__, fn, mode)

#define xassert(cond, msg) if ((cond) == 0) _err_fatal_simple_core(__func__, msg)

#if defined(__GNUC__) && __GNUC__ < 11 && !defined(__clang__)
#if defined(__i386__)
static inline unsigned long long __rdtsc(void)
{
	unsigned long long int x;
	__asm__ volatile(".byte 0x0f, 0x31" : "=A"(x));
	return x;
}
#elif defined(__x86_64__)
static inline unsigned long long __rdtsc(void)
{
	unsigned hi, lo;
	__asm__ __volatile__("rdtsc" : "=a"(lo), "=d"(hi));
	return ((unsigned long long)lo) | (((unsigned long long)hi) << 32);
}
#endif
#endif

typedef struct {
	uint64_t x, y;
} pair64_t;

typedef struct { size_t n, m; uint64_t *a; } uint64_v;
typedef struct { size_t n, m; uint32_t *a; } uint32_v;
typedef struct { size_t n, m; pair64_t *a; } pair64_v;

typedef struct { size_t m; uint8_t *addr; } buf_t;

#ifdef __cplusplus
extern "C" {
#endif

	void err_fatal(const char *header, const char *fmt, ...) ATTRIBUTE((noreturn));
	void err_fatal_core(const char *header, const char *fmt, ...) ATTRIBUTE((noreturn));
	void _err_fatal_simple(const char *func, const char *msg) ATTRIBUTE((noreturn));
	void _err_fatal_simple_core(const char *func, const char *msg) ATTRIBUTE((noreturn));
	FILE *err_xopen_core(const char *func, const char *fn, const char *mode);
	FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp);
	gzFile err_xzopen_core(const char *func, const char *fn, const char *mode);
    size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream);
	size_t err_fread_noeof(void *ptr, size_t size, size_t nmemb, FILE *stream);
	uint64_t fread_fix(FILE *fp, uint64_t size, void *a);

	int err_gzread(gzFile file, void *ptr, unsigned int len);
	int err_fseek(FILE *stream, long offset, int whence);
#define err_rewind(FP) err_fseek((FP), 0, SEEK_SET)
	long err_ftell(FILE *stream);
	int err_fprintf(FILE *stream, const char *format, ...)
        ATTRIBUTE((format(printf, 2, 3)));
	int err_printf(const char *format, ...)
        ATTRIBUTE((format(printf, 1, 2)));
	int err_fputc(int c, FILE *stream);
#define err_putchar(C) err_fputc((C), stdout)
	int err_fputs(const char *s, FILE *stream);
	int err_puts(const char *s);
	int err_fflush(FILE *stream);
	int err_fclose(FILE *stream);
	int err_gzclose(gzFile file);

	double cputime(void);
	double realtime(void);
	uint64_t realtime_msec(void);
	long peakrss(void);

	void ks_introsort_64 (size_t n, uint64_t *a);
	void ks_introsort_128(size_t n, pair64_t *a);

#ifdef __cplusplus
}
#endif

static inline uint64_t hash_64(uint64_t key)
{
	key += ~(key << 32);
	key ^= (key >> 22);
	key += ~(key << 13);
	key ^= (key >> 8);
	key += (key << 3);
	key ^= (key >> 15);
	key += ~(key << 27);
	key ^= (key >> 31);
	return key;
}

#endif