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#define _DEFAULT_SOURCE // expose MADV_RANDOM etc. under -std=c99 (glibc >= 2.19)

#define _BSD_SOURCE // ditto on older glibc (e.g. CentOS 7 / glibc 2.17)

#include <stdlib.h>

#include <string.h>

#include <stdarg.h>

#include <stdio.h>

#include "kommon.h"

int kom_verbose = 3, kom_dbg = 0, kom_dbg_flag = 0;

char *kom_strdup(const char *src) // strdup() doesn't conform to C99

{

size_t len;

char *dst;

len = strlen(src);

dst = kom_malloc(char, len + 1);

memcpy(dst, src, len + 1);

return dst;

}

int64_t kom_parse_num(const char *str, char **q)

{

double x;

char *p;

x = strtod(str, &p);

if (*p == 'G' || *p == 'g') x *= 1e9, ++p;

else if (*p == 'M' || *p == 'm') x *= 1e6, ++p;

else if (*p == 'K' || *p == 'k') x *= 1e3, ++p;

if (q) *q = p;

return (int64_t)(x + .499);

}

void kom_panic(const char *func, const char *msg)

{

fprintf(stderr, "[E::%s] %s ABORT!\n", func, msg);

abort();

}

/****************

* Fast sprintf *

****************/

#ifdef HAVE_KALLOC

#include "kalloc.h"

#endif

static inline void str_enlarge(void *km, kstring_t *s, int l)

{

if (s->l + l + 1 > s->m) {

s->m = s->l + l + 1;

kom_roundup64(s->m);

#ifdef HAVE_KALLOC

s->s = Krealloc(km, char, s->s, s->m);

#else

s->s = kom_realloc(char, s->s, s->m);

#endif

}

static inline void str_copy(void *km, kstring_t *s, const char *st, const char *en)

{

str_enlarge(km, s, en - st);

memcpy(&s->s[s->l], st, en - st);

s->l += en - st;

}

int64_t kom_sprintf_lite_core(void *km, kstring_t *s, const char *fmt, va_list ap)

{

char buf[32]; // for integer to string conversion

const char *p, *q;

int64_t len = 0;

for (q = p = fmt; *p; ++p) {

if (*p == '%') {

if (p > q) {

len += p - q;

if (s) str_copy(km, s, q, p);

}

++p;

if (*p == 'd') {

int c, i, l = 0;

unsigned int x;

c = va_arg(ap, int);

x = c >= 0? c : -c;

do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);

if (c < 0) buf[l++] = '-';

len += l;

if (s) {

str_enla 10BC8 rge(km, s, l);

for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];

}

} else if (*p == 'l' && *(p+1) == 'd') {

int i, l = 0;

long c;

unsigned long x;

c = va_arg(ap, long);

x = c >= 0? c : -c;

do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);

if (c < 0) buf[l++] = '-';

len += l;

if (s) {

str_enlarge(km, s, l);

for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];

}

++p;

} else if (*p == 'u') {

int i, l = 0;

uint32_t x;

x = va_arg(ap, uint32_t);

do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);

len += l;

if (s) {

str_enlarge(km, s, l);

for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];

}

} else if (*p == 's') {

char *r = va_arg(ap, char*);

int l;

l = strlen(r);

len += l;

if (s) str_copy(km, s, r, r + l);

} else if (*p == 'c') {

++len;

if (s) {

str_enlarge(km, s, 1);

s->s[s->l++] = va_arg(ap, int);

}

} else {

fprintf(stderr, "ERROR: unrecognized type '%%%c'\n", *p);

abort();

}

q = p + 1;

}

if (p > q) {

len += p - q;

if (s) str_copy(km, s, q, p);

}

if (s) s->s[s->l] = 0;

return len;

}

int64_t kom_sprintf_lite(kstring_t *s, const char *fmt, ...)

{

int64_t ret;

va_list ap;

va_start(ap, fmt); ret = kom_sprintf_lite_core(0, s, fmt, ap); va_end(ap);

return ret;

}

int64_t km_sprintf_lite(void *km, kstring_t *s, const char *fmt, ...)

{

int64_t ret;

va_list ap;

va_start(ap, fmt); ret = kom_sprintf_lite_core(km, s, fmt, ap); va_end(ap);

return ret;

}

/****************

* DNA sequence *

****************/

uint8_t kom_nt4_table[256] = {

0, 1, 2, 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, 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

};

uint8_t kom_comp_table[256] = {

3, 2, 1, 0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,

16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,

32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,

48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,

64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',

'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95,

96, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',

'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127,

128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,

144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,

160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,

176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,

192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,

208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,

224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,

240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255

};

void kom_revcomp(uint64_t len, char *seq) // reverse complement in place

{

uint64_t i;

for (i = 0; i < len>>1; ++i) {

uint8_t t = seq[len - i - 1];

seq[len - i - 1] = kom_comp_table[(uint8_t)seq[i]];

seq[i] = kom_comp_table[t];

}

if (len&1) seq[len>>1] = kom_comp_table[(uint8_t)seq[len>>1]];

}

/***********************

* Timing and peak RSS *

***********************/

#if defined(WIN32) || defined(_WIN32)

#include <windows.h>

struct timezone

{

__int32 tz_minuteswest; /* minutes W of Greenwich */

int tz_dsttime; /* type of dst correction */

};

* gettimeofday.c

* Win32 gettimeofday() replacement

* taken from PostgreSQL, according to

* https://stackoverflow.com/questions/1676036/what-should-i-use-to-replace-gettimeofday-on-windows

* src/port/gettimeofday.c

* Permission to use, copy, modify, and distribute this software and

* its documentation for any purpose, without fee, and without a

* written agreement is hereby granted, provided that the above

* copyright notice and this paragraph and the following two

* paragraphs appear in all copies.

* IN NO EVENT SHALL THE AUTHOR BE LIABLE TO ANY PARTY FOR DIRECT,

* INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING

* LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS

* DOCUMENTATION, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED

* OF THE POSSIBILITY OF SUCH DAMAGE.

* THE AUTHOR SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT

* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

* A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS

* IS" BASIS, AND THE AUTHOR HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE,

* SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

/* FILETIME of Jan 1 1970 00:00:00. */

static const unsigned __int64 epoch = ((unsigned __int64) 116444736000000000ULL);

* timezone information is stored outside the kernel so tzp isn't used anymore.

* Note: this function is not for Win32 high precision timing purpose. See

* elapsed_time().

int gettimeofday(struct timeval * tp, struct timezone *tzp)

{

FILETIME file_time;

SYSTEMTIME system_time;

ULARGE_INTEGER ularge;

GetSystemTime(&system_time);

SystemTimeToFileTime(&system_time, &file_time);

ularge.LowPart = file_time.dwLowDateTime;

ularge.HighPart = file_time.dwHighDateTime;

tp->tv_sec = (long) ((ularge.QuadPart - epoch) / 10000000L);

tp->tv_usec = (long) (system_time.wMilliseconds * 1000);

return 0;

}

// taken from https://stackoverflow.com/questions/5272470/c-get-cpu-usage-on-linux-and-windows

double kom_cputime()

{

HANDLE hProcess = GetCurrentProcess();

FILETIME ftCreation, ftExit, ftKernel, ftUser;

SYSTEMTIME stKernel;

SYSTEMTIME stUser;

GetProcessTimes(hProcess, &ftCreation, &ftExit, &ftKernel, &ftUser);

FileTimeToSystemTime(&ftKernel, &stKernel);

FileTimeToSystemTime(&ftUser, &stUser);

double kernelModeTime = ((stKernel.wHour * 60.) + stKernel.wMinute * 60.) + stKernel.wSecond * 1. + stKernel.wMilliseconds / 1000.;

double userModeTime = ((stUser.wHour * 60.) + stUser.wMinute * 60.) + stUser.wSecond * 1. + stUser.wMilliseconds / 1000.;

return kernelModeTime + userModeTime;

}

long kom_peakrss(void) { return 0; }

#else

#include <sys/resource.h>

#include <sys/time.h>

double kom_cputime(void)

{

struct rusage r;

getrusage(RUSAGE_SELF, &r);

return r.ru_utime.tv_sec + r.ru_stime.tv_sec + 1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);

}

long kom_peakrss(void)

{

struct rusage r;

getrusage(RUSAGE_SELF, &r);

#ifdef __linux__

return r.ru_maxrss * 1024;

#else

return r.ru_maxrss;

#endif

}

#endif /* WIN32 || _WIN32 */

double kom_realtime(void)

{

static double realtime0 = -1.0;

struct timeval tp;

double t;

gettimeofday(&tp, NULL);

t = tp.tv_sec + tp.tv_usec * 1e-6;

if (realtime0 < 0.0) realtime0 = t;

return t - realtime0;

}

double kom_percent_cpu(void)

{

return (kom_cputime() + 1e-6) / (kom_realtime() + 1e-6);

}

/***************

* mmap loader *

***************/

#include <fcntl.h>

#include <unistd.h>

#include <sys/mman.h>

#include <sys/stat.h>

void *kom_mmap_file(const char *fn, size_t *len, int preload)

{

int fd, mmap_flags = MAP_SHARED;

struct stat st;

uint8_t *base;

*len = 0;

fd = open(fn, O_RDONLY);

if (fd < 0) return 0;

if (fstat(fd, &st) < 0 || st.st_size == 0) { close(fd); return 0; }

*len = st.st_size;

#ifdef MAP_POPULATE // this is Linux only

if (preload) mmap_flags |= MAP_POPULATE;

#endif

base = (uint8_t*)mmap(0, *len, PROT_READ, mmap_flags, fd, 0);

close(fd);

if (base == MAP_FAILED) return 0;

#ifdef MADV_RANDOM

madvise(base, *len, MADV_RANDOM);

#endif

return base;

}

int kom_munmap(void *base, size_t map_len) // a simple wrapper

{

return munmap(base, map_len);

}

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