1 2 3 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 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641
|
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#include <sysalloc.h>
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <ctype.h>
#include <kapp/main.h>
#include <kapp/args.h>
#include <klib/rc.h>
#include <klib/out.h>
#include <klib/log.h>
#include <klib/text.h>
#include <klib/printf.h>
#include <kapp/log-xml.h>
#include <align/writer-refseq.h>
#include <insdc/sra.h>
#include <sra/sradb.h>
#include "common-writer.h"
#include "fastq-parse.h"
extern rc_t run(char const argv0[],
struct CommonWriterSettings* G,
unsigned countReads,
const char* reads[],
enum FASTQQualityFormat qualityFormat,
const int8_t defaultReadNumbers[],
bool ignoreSpotGroups);
/* MARK: Arguments and Usage */
//static char const option_input[] = "input";
static char const option_output[] = "output";
static char const option_tmpfs[] = "tmpfs";
static char const option_qual_compress[] = "qual-quant";
static char const option_cache_size[] = "cache-size";
static char const option_max_err_count[] = "max-err-count";
static char const option_max_rec_count[] = "max-rec-count";
static char const option_platform[] = "platform";
static char const option_quality[] = "quality";
//static char const option_read[] = "read";
static char const option_max_err_pct[] = "max-err-pct";
static char const option_ignore_illumina_tags[] = "ignore-illumina-tags";
static char const option_no_readnames[] = "no-readnames";
#define OPTION_INPUT option_input
#define OPTION_OUTPUT option_output
#define OPTION_TMPFS option_tmpfs
#define OPTION_QCOMP option_qual_compress
#define OPTION_CACHE_SIZE option_cache_size
#define OPTION_MAX_ERR_COUNT option_max_err_count
#define OPTION_MAX_REC_COUNT option_max_rec_count
#define OPTION_PLATFORM option_platform
#define OPTION_QUALITY option_quality
#define OPTION_READ option_read
#define OPTION_MAX_ERR_PCT option_max_err_pct
#define OPTION_IGNORE_ILLUMINA_TAGS option_ignore_illumina_tags
#define OPTION_NO_READNAMES option_no_readnames
#define ALIAS_INPUT "i"
#define ALIAS_OUTPUT "o"
#define ALIAS_TMPFS "t"
#define ALIAS_QCOMP "Q"
#define ALIAS_MAX_ERR_COUNT "E"
#define ALIAS_PLATFORM "p"
#define ALIAS_READ "r"
/* this alias is deprecated (conflicts with -q for --quiet): */
#define ALIAS_QUALITY "q"
static
char const * output_usage[] =
{
"Path and Name of the output database.",
NULL
};
static
char const * tmpfs_usage[] =
{
"Path to be used for scratch files.",
NULL
};
static
char const * qcomp_usage[] =
{
"Quality scores quantization level, can be a number (0: none - default, 1: 2bit, 2: 1bit), or a string like '1:10,10:20,20:30,30:-' (which is equivalent to 1).",
NULL
};
static
char const * cache_size_usage[] =
{
"Set the cache size in MB for the temporary indices",
NULL
};
static
char const * mrc_usage[] =
{
"Set the maximum number of records to process from the FASTQ file",
NULL
};
static
char const * mec_usage[] =
{
"Set the maximum number of errors to ignore from the FASTQ file",
NULL
};
static
char const * use_platform[] =
{
"Platform (ILLUMINA, LS454, SOLID, COMPLETE_GENOMICS, HELICOS, PACBIO, IONTORRENT, CAPILLARY)",
NULL
};
static
char const * use_quality[] =
{
"Quality encoding (PHRED_33, PHRED_64, LOGODDS)",
NULL
};
/*static
char const * use_read[] =
{
"Default read number (1 or 2)",
NULL
};*/
static
char const * use_max_err_pct[] =
{
"acceptable percentage of spots creation errors, default is 5",
NULL
};
static
char const * use_ignore_illumina_tags[] =
{
"ignore barcodes contained in Illumina-formatted names",
NULL
};
static
char const * use_no_readnames[] =
{
"drop original read names",
NULL
};
OptDef Options[] =
{
/* order here is same as in param array below!!! */ /* max#, needs param, required */
{ OPTION_OUTPUT, ALIAS_OUTPUT, NULL, output_usage, 1, true, true },
{ OPTION_TMPFS, ALIAS_TMPFS, NULL, tmpfs_usage, 1, true, false },
{ OPTION_QCOMP, ALIAS_QCOMP, NULL, qcomp_usage, 1, true, false },
{ OPTION_CACHE_SIZE, NULL, NULL, cache_size_usage, 1, true, false },
{ OPTION_MAX_REC_COUNT, NULL, NULL, mrc_usage, 1, true, false },
{ OPTION_MAX_ERR_COUNT, ALIAS_MAX_ERR_COUNT, NULL, mec_usage, 1, true, false },
{ OPTION_PLATFORM, ALIAS_PLATFORM, NULL, use_platform, 1, true, false },
{ OPTION_QUALITY, ALIAS_QUALITY, NULL, use_quality, 1, true, true },
{ OPTION_MAX_ERR_PCT, NULL, NULL, use_max_err_pct, 1, true, false },
{ OPTION_IGNORE_ILLUMINA_TAGS, NULL, NULL, use_ignore_illumina_tags, 1, false, false },
{ OPTION_NO_READNAMES, NULL, NULL, use_no_readnames, 1, false, false },
/* { OPTION_READ, ALIAS_READ, NULL, use_read, 0, true, false },*/
};
const char* OptHelpParam[] =
{
/* order here is same as in OptDef array above!!! */
"path",
"path-to-file",
"phred-score",
"mbytes",
"count",
"count",
NULL,
NULL,
NULL,
NULL,
NULL,
};
rc_t UsageSummary (char const * progname)
{
return KOutMsg (
"Usage:\n"
"\t%s [options] <fastq-file> ...\n"
"\n"
"Summary:\n"
"\tLoad FASTQ formatted data files\n"
"\n"
"Example:\n"
"\t%s -p 454 -o /tmp/SRZ123456 123456-1.fastq 123456-2.fastq\n"
"\n"
,progname, progname);
}
char const UsageDefaultName[] = "fastq-load";
rc_t CC Usage (const Args * args)
{
rc_t rc;
int i;
const char * progname = UsageDefaultName;
const char * fullpath = UsageDefaultName;
const size_t argsQty = sizeof(Options) / sizeof(Options[0]);
if (args == NULL)
rc = RC (rcApp, rcArgv, rcAccessing, rcSelf, rcNull);
else
rc = ArgsProgram (args, &fullpath, &progname);
if (rc)
progname = fullpath = UsageDefaultName;
UsageSummary (progname);
for(i = 0; i < argsQty; i++ ) {
if( Options[i].required && Options[i].help[0] != NULL ) {
HelpOptionLine(Options[i].aliases, Options[i].name, OptHelpParam[i], Options[i].help);
}
}
OUTMSG(("\nOptions:\n"));
for(i = 0; i < argsQty; i++ ) {
if( !Options[i].required && Options[i].help[0] != NULL ) {
HelpOptionLine(Options[i].aliases, Options[i].name, OptHelpParam[i], Options[i].help);
}
}
XMLLogger_Usage();
OUTMSG(("\n"));
HelpOptionsStandard ();
HelpVersion (fullpath, KAppVersion());
return rc;
}
/* MARK: Definitions and Globals */
#define SCHEMAFILE "/usr/lib/ncbi-vdb/align/align.vschema"
CommonWriterSettings G;
#ifdef _WIN32
#include <process.h>
#else
#include <unistd.h>
#endif
static void set_pid(void)
{
G.pid = getpid();
}
static bool platform_cmp(char const platform[], char const test[])
{
unsigned i;
for (i = 0; ; ++i) {
int ch1 = test[i];
int ch2 = toupper(platform[i]);
if (ch1 != ch2)
break;
if (ch1 == 0)
return true;
}
return false;
}
static INSDC_SRA_platform_id PlatformToId(const char* name)
{
if (name != NULL)
{
switch (toupper(name[0])) {
case 'C':
if (platform_cmp(name, "CAPILLARY"))
return SRA_PLATFORM_CAPILLARY;
if (platform_cmp(name, "COMPLETE GENOMICS") || platform_cmp(name, "COMPLETE_GENOMICS"))
return SRA_PLATFORM_COMPLETE_GENOMICS;
break;
case 'H':
if (platform_cmp(name, "HELICOS"))
return SRA_PLATFORM_HELICOS;
break;
case 'I':
if (platform_cmp(name, "ILLUMINA"))
return SRA_PLATFORM_ILLUMINA;
if (platform_cmp(name, "IONTORRENT"))
return SRA_PLATFORM_ION_TORRENT;
break;
case 'L':
if (platform_cmp(name, "LS454"))
return SRA_PLATFORM_454;
break;
case 'N':
if (platform_cmp(name, "NANOPORE"))
return SRA_PLATFORM_OXFORD_NANOPORE;
break;
case 'O':
if (platform_cmp(name, "OXFORD_NANOPORE"))
return SRA_PLATFORM_OXFORD_NANOPORE;
break;
case 'P':
if (platform_cmp(name, "PACBIO"))
return SRA_PLATFORM_PACBIO_SMRT;
break;
case 'S':
if (platform_cmp(name, "SOLID"))
return SRA_PLATFORM_ABSOLID;
if (platform_cmp(name, "SANGER"))
return SRA_PLATFORM_CAPILLARY;
break;
default:
break;
}
}
return SRA_PLATFORM_UNDEFINED;
}
static rc_t PathWithBasePath(char rslt[], size_t sz, char const path[], char const base[])
{
size_t const plen = strlen(path);
bool const hasBase = base && base[0];
bool const isBareName = strchr(path, '/') == NULL;
if (isBareName && hasBase) {
if (string_printf(rslt, sz, NULL, "%s/%s", base, path) == 0)
return 0;
}
else if ( string_copy ( rslt, sz, path, plen ) < sz )
return 0;
{
rc_t const rc = RC(rcApp, rcArgv, rcAccessing, rcBuffer, rcInsufficient);
(void)LOGERR(klogErr, rc, "The path to the file is too long");
return rc;
}
}
rc_t CC KMain (int argc, char * argv[])
{
Args * args;
rc_t rc;
char *files[256];
int8_t defaultReadNumbers[256];
char *name_buffer = NULL;
size_t next_name = 0;
size_t nbsz = 0;
char const *value;
char *dummy;
const XMLLogger* xml_logger = NULL;
enum FASTQQualityFormat qualityFormat;
bool ignoreSpotGroups;
memset(&G, 0, sizeof(G));
G.maxSeqLen = TableWriterRefSeq_MAX_SEQ_LEN;
G.schemaPath = SCHEMAFILE;
G.omit_aligned_reads = true;
G.omit_reference_reads = true;
G.minMapQual = 0; /* accept all */
G.tmpfs = "/tmp";
#if _ARCH_BITS == 32
G.cache_size = ( size_t ) 1 << 30;
#else
G.cache_size = ( size_t ) 10 << 30;
#endif
G.maxErrCount = 1000;
G.maxErrPct = 5;
G.acceptNoMatch = true;
G.minMatchCount = 0;
G.QualQuantizer="0";
set_pid();
rc = ArgsMakeAndHandle (&args, argc, argv, 2, Options,
sizeof Options / sizeof (OptDef), XMLLogger_Args, XMLLogger_ArgsQty);
while (rc == 0) {
uint32_t pcount;
if( (rc = XMLLogger_Make(&xml_logger, NULL, args)) != 0 ) {
break;
}
rc = ArgsOptionCount (args, OPTION_TMPFS, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_TMPFS, 0, (const void **)&G.tmpfs);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_OUTPUT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_OUTPUT, 0, (const void **)&G.outpath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single output parameter required\n"));
MiniUsage (args);
break;
}
else {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
OUTMSG (("Output parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_QCOMP, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_QCOMP, 0, (const void **)&G.QualQuantizer);
if (rc)
break;
}
rc = ArgsOptionCount (args, OPTION_CACHE_SIZE, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_CACHE_SIZE, 0, (const void **)&value);
if (rc)
break;
G.cache_size = strtoul(value, &dummy, 0) * 1024UL * 1024UL;
if (G.cache_size == 0 || G.cache_size == ULONG_MAX) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
OUTMSG (("cache-size: bad value\n"));
MiniUsage (args);
break;
}
}
G.expectUnsorted = true;
rc = ArgsOptionCount (args, OPTION_MAX_REC_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_REC_COUNT, 0, (const void **)&value);
if (rc)
break;
G.maxAlignCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MAX_ERR_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_ERR_COUNT, 0, (const void **)&value);
if (rc)
break;
G.maxErrCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MAX_ERR_PCT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_ERR_PCT, 0, (const void **)&value);
if (rc)
break;
G.maxErrPct = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_PLATFORM, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_PLATFORM, 0, (const void **)&value);
if (rc)
break;
G.platform = PlatformToId(value);
if (G.platform == SRA_PLATFORM_UNDEFINED)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
(void)PLOGERR(klogErr, (klogErr, rc, "Invalid platform $(v)",
"v=%s", value));
break;
}
}
else
G.platform = SRA_PLATFORM_UNDEFINED;
rc = ArgsOptionCount (args, OPTION_QUALITY, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_QUALITY, 0, (const void **)&value);
if (rc)
break;
if (strcmp(value, "PHRED_33") == 0)
qualityFormat = FASTQphred33;
else if (strcmp(value, "PHRED_64") == 0)
qualityFormat = FASTQphred64;
else if (strcmp(value, "LOGODDS") == 0)
qualityFormat = FASTQlogodds;
else
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
(void)PLOGERR(klogErr, (klogErr, rc, "Invalid quality encoding $(v)",
"v=%s", value));
break;
}
}
else
qualityFormat = 0;
rc = ArgsOptionCount (args, OPTION_IGNORE_ILLUMINA_TAGS, &pcount);
if (rc)
break;
ignoreSpotGroups = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NO_READNAMES, &pcount);
if (rc)
break;
G.dropReadnames = pcount > 0;
rc = ArgsParamCount (args, &pcount);
if (rc) break;
if (pcount == 0)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
MiniUsage (args);
break;
}
else if (pcount > sizeof(files)/sizeof(files[0])) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
(void)PLOGERR(klogErr, (klogErr, rc, "$(count) input files is too many, $(max) is the limit",
"count=%u,max=%u", (unsigned)pcount, (unsigned)(sizeof(files)/sizeof(files[0]))));
break;
}
else {
size_t need = G.inpath ? (strlen(G.inpath) + 1) * pcount : 0;
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, (const void **)&value);
if (rc) break;
need += strlen(value) + 1;
}
nbsz = need;
}
name_buffer = malloc(nbsz);
if (name_buffer == NULL) {
rc = RC(rcApp, rcArgv, rcAccessing, rcMemory, rcExhausted);
break;
}
rc = ArgsParamCount (args, &pcount);
if (rc == 0) {
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, (const void **)&value);
if (rc) break;
defaultReadNumbers[i] = 0;
files[i] = name_buffer + next_name;
rc = PathWithBasePath(name_buffer + next_name, nbsz - next_name, value, G.inpath);
if (rc) break;
next_name += strlen(name_buffer + next_name) + 1;
}
}
else
break;
rc = run(argv[0], &G, pcount, (char const **)files, qualityFormat, defaultReadNumbers, ignoreSpotGroups);
break;
}
free(name_buffer);
value = G.outpath ? strrchr(G.outpath, '/') : "/???";
if( value == NULL ) {
value = G.outpath;
} else {
value++;
}
if (rc) {
(void)PLOGERR(klogErr, (klogErr, rc, "load failed",
"severity=total,status=failure,accession=%s,errors=%u", value, G.errCount));
} else {
(void)PLOGMSG(klogInfo, (klogInfo, "loaded",
"severity=total,status=success,accession=%s,errors=%u", value, G.errCount));
}
ArgsWhack(args);
XMLLogger_Release(xml_logger);
return rc;
}
|