minibwa/kommon.c at avx2 · nh13/minibwa

Repository navigation

History

100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

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

256

257

258

259

260

261

262

263

264

265

266

267

268

269

270

271

272

273

274

275

276

277

278

279

280

281

282

283

284

285

286

287

288

289

290

291

292

293

294

295

296

297

298

299

300

301

302

303

304

305

306

307

308

309

310

311

312

313

314

315

316

317

318

319

320

321

322

323

324

325

326

327

328

329

330

331

332

333

334

335

#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_enlarge(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);

}

FilesExpand file tree

kommon.c

Latest commit

History

kommon.c

File metadata and controls