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minimap2/main.c
Saurabh 0369874d4e mm2-fast: Initial commit
2021-06-16 15:50:17 -04:00

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/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
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.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <string>
#include <errno.h>
#include "bseq.h"
#include "minimap.h"
#include "mmpriv.h"
#include "ketopt.h"
#include <x86intrin.h>
#define MM_VERSION "2.18-r1015"
using namespace std;
#ifdef MANUAL_PROFILING
uint64_t num_reads = 0, minimizer_hit_time = 0, dp_chaining_time = 0, alignment_time = 0;
#endif
#ifdef LISA_HASH
#include "lisa_hash.h"
lisa_hash<uint64_t, uint64_t> *lh;
#endif
#ifdef __linux__
#include <sys/resource.h>
#include <sys/time.h>
void liftrlimit()
{
struct rlimit r;
getrlimit(RLIMIT_AS, &r);
r.rlim_cur = r.rlim_max;
setrlimit(RLIMIT_AS, &r);
}
#else
void liftrlimit() {}
#endif
static ko_longopt_t long_options[] = {
{ "bucket-bits", ko_required_argument, 300 },
{ "mb-size", ko_required_argument, 'K' },
{ "seed", ko_required_argument, 302 },
{ "no-kalloc", ko_no_argument, 303 },
{ "print-qname", ko_no_argument, 304 },
{ "no-self", ko_no_argument, 'D' },
{ "print-seeds", ko_no_argument, 306 },
{ "max-chain-skip", ko_required_argument, 307 },
{ "min-dp-len", ko_required_argument, 308 },
{ "print-aln-seq", ko_no_argument, 309 },
{ "splice", ko_no_argument, 310 },
{ "cost-non-gt-ag", ko_required_argument, 'C' },
{ "no-long-join", ko_no_argument, 312 },
{ "sr", ko_no_argument, 313 },
{ "frag", ko_required_argument, 314 },
{ "secondary", ko_required_argument, 315 },
{ "cs", ko_optional_argument, 316 },
{ "end-bonus", ko_required_argument, 317 },
{ "no-pairing", ko_no_argument, 318 },
{ "splice-flank", ko_required_argument, 319 },
{ "idx-no-seq", ko_no_argument, 320 },
{ "end-seed-pen", ko_required_argument, 321 },
{ "for-only", ko_no_argument, 322 },
{ "rev-only", ko_no_argument, 323 },
{ "heap-sort", ko_required_argument, 324 },
{ "all-chain", ko_no_argument, 'P' },
{ "dual", ko_required_argument, 326 },
{ "max-clip-ratio", ko_required_argument, 327 },
{ "min-occ-floor", ko_required_argument, 328 },
{ "MD", ko_no_argument, 329 },
{ "lj-min-ratio", ko_required_argument, 330 },
{ "score-N", ko_required_argument, 331 },
{ "eqx", ko_no_argument, 332 },
{ "paf-no-hit", ko_no_argument, 333 },
{ "split-prefix", ko_required_argument, 334 },
{ "no-end-flt", ko_no_argument, 335 },
{ "hard-mask-level",ko_no_argument, 336 },
{ "cap-sw-mem", ko_required_argument, 337 },
{ "max-qlen", ko_required_argument, 338 },
{ "max-chain-iter", ko_required_argument, 339 },
{ "junc-bed", ko_required_argument, 340 },
{ "junc-bonus", ko_required_argument, 341 },
{ "sam-hit-only", ko_no_argument, 342 },
{ "chain-gap-scale",ko_required_argument, 343 },
{ "alt", ko_required_argument, 344 },
{ "alt-drop", ko_required_argument, 345 },
{ "mask-len", ko_required_argument, 346 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
{ "min-count", ko_required_argument, 'n' },
{ "min-chain-score",ko_required_argument, 'm' },
{ "mask-level", ko_required_argument, 'M' },
{ "min-dp-score", ko_required_argument, 's' },
{ "sam", ko_no_argument, 'a' },
{ 0, 0, 0 }
};
static inline int64_t mm_parse_num(const char *str)
{
double x;
char *p;
x = strtod(str, &p);
if (*p == 'G' || *p == 'g') x *= 1e9;
else if (*p == 'M' || *p == 'm') x *= 1e6;
else if (*p == 'K' || *p == 'k') x *= 1e3;
return (int64_t)(x + .499);
}
static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const char *arg, int yes_to_set)
{
if (yes_to_set) {
if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) opt->flag |= flag;
else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) opt->flag &= ~flag;
else fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
} else {
if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) opt->flag &= ~flag;
else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) opt->flag |= flag;
else fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
}
}
int main(int argc, char *argv[])
{
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:Z:";
ketopt_t o = KETOPT_INIT;
mm_mapopt_t opt;
mm_idxopt_t ipt;
int i, c, n_threads = 3, n_parts, old_best_n = -1;
uint64_t total_time = 0;
char *fnw = 0, *rg = 0, *junc_bed = 0, *s, *alt_list = 0;
FILE *fp_help = stderr;
mm_idx_reader_t *idx_rdr;
mm_idx_t *mi;
mm_verbose = 3;
liftrlimit();
mm_realtime0 = realtime();
mm_set_opt(0, &ipt, &opt);
string preset_arg = "";
while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) { // test command line options and apply option -x/preset first
if (c == 'x') {
preset_arg += (string) o.arg;
if (mm_set_opt(o.arg, &ipt, &opt) < 0) {
fprintf(stderr, "[ERROR] unknown preset '%s'\n", o.arg);
return 1;
}
} else if (c == ':') {
fprintf(stderr, "[ERROR] missing option argument\n");
return 1;
} else if (c == '?') {
fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[o.i - 1]);
return 1;
}
}
o = KETOPT_INIT;
while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) {
if (c == 'w') ipt.w = atoi(o.arg);
else if (c == 'Z') opt.L_hash = atoi(o.arg);
else if (c == 'k') ipt.k = atoi(o.arg);
else if (c == 'H') ipt.flag |= MM_I_HPC;
else if (c == 'd') fnw = o.arg; // the above are indexing related options, except -I
else if (c == 'r') opt.bw = (int)mm_parse_num(o.arg);
else if (c == 't') n_threads = atoi(o.arg);
else if (c == 'v') mm_verbose = atoi(o.arg);
else if (c == 'g') opt.max_gap = (int)mm_parse_num(o.arg);
else if (c == 'G') mm_mapopt_max_intron_len(&opt, (int)mm_parse_num(o.arg));
else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(o.arg);
else if (c == 'N') old_best_n = opt.best_n, opt.best_n = atoi(o.arg);
else if (c == 'p') opt.pri_ratio = atof(o.arg);
else if (c == 'M') opt.mask_level = atof(o.arg);
else if (c == 'c') opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
else if (c == 'D') opt.flag |= MM_F_NO_DIAG;
else if (c == 'P') opt.flag |= MM_F_ALL_CHAINS;
else if (c == 'X') opt.flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN; // -D -P --no-long-join --dual=no
else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
else if (c == 'Y') opt.flag |= MM_F_SOFTCLIP;
else if (c == 'L') opt.flag |= MM_F_LONG_CIGAR;
else if (c == 'y') opt.flag |= MM_F_COPY_COMMENT;
else if (c == 'T') opt.sdust_thres = atoi(o.arg);
else if (c == 'n') opt.min_cnt = atoi(o.arg);
else if (c == 'm') opt.min_chain_score = atoi(o.arg);
else if (c == 'A') opt.a = atoi(o.arg);
else if (c == 'B') opt.b = atoi(o.arg);
else if (c == 's') opt.min_dp_max = atoi(o.arg);
else if (c == 'C') opt.noncan = atoi(o.arg);
else if (c == 'I') ipt.batch_size = mm_parse_num(o.arg);
else if (c == 'K') opt.mini_batch_size = mm_parse_num(o.arg);
else if (c == 'R') rg = o.arg;
else if (c == 'h') fp_help = stdout;
else if (c == '2') opt.flag |= MM_F_2_IO_THREADS;
else if (c == 'o') {
if (strcmp(o.arg, "-") != 0) {
if (freopen(o.arg, "wb", stdout) == NULL) {
fprintf(stderr, "[ERROR]\033[1;31m failed to write the output to file '%s'\033[0m: %s\n", o.arg, strerror(errno));
exit(1);
}
}
}
else if (c == 300) ipt.bucket_bits = atoi(o.arg); // --bucket-bits
else if (c == 302) opt.seed = atoi(o.arg); // --seed
else if (c == 303) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
else if (c == 304) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
else if (c == 306) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED, n_threads = 1; // --print-seed
else if (c == 307) opt.max_chain_skip = atoi(o.arg); // --max-chain-skip
else if (c == 339) opt.max_chain_iter = atoi(o.arg); // --max-chain-iter
else if (c == 308) opt.min_ksw_len = atoi(o.arg); // --min-dp-len
else if (c == 309) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ, n_threads = 1; // --print-aln-seq
else if (c == 310) opt.flag |= MM_F_SPLICE; // --splice
else if (c == 312) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
else if (c == 313) opt.flag |= MM_F_SR; // --sr
else if (c == 317) opt.end_bonus = atoi(o.arg); // --end-bonus
else if (c == 318) opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing
else if (c == 320) ipt.flag |= MM_I_NO_SEQ; // --idx-no-seq
else if (c == 321) opt.anchor_ext_shift = atoi(o.arg); // --end-seed-pen
else if (c == 322) opt.flag |= MM_F_FOR_ONLY; // --for-only
else if (c == 323) opt.flag |= MM_F_REV_ONLY; // --rev-only
else if (c == 327) opt.max_clip_ratio = atof(o.arg); // --max-clip-ratio
else if (c == 328) opt.min_mid_occ = atoi(o.arg); // --min-occ-floor
else if (c == 329) opt.flag |= MM_F_OUT_MD; // --MD
else if (c == 330) opt.min_join_flank_ratio = atof(o.arg); // --lj-min-ratio
else if (c == 331) opt.sc_ambi = atoi(o.arg); // --score-N
else if (c == 332) opt.flag |= MM_F_EQX; // --eqx
else if (c == 333) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
else if (c == 334) opt.split_prefix = o.arg; // --split-prefix
else if (c == 335) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
else if (c == 336) opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level
else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
else if (c == 340) junc_bed = o.arg; // --junc-bed
else if (c == 341) opt.junc_bonus = atoi(o.arg); // --junc-bonus
else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
else if (c == 343) opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
else if (c == 344) alt_list = o.arg; // --alt
else if (c == 345) opt.alt_drop = atof(o.arg); // --alt-drop
else if (c == 346) opt.mask_len = mm_parse_num(o.arg); // --mask-len
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary
yes_or_no(&opt, MM_F_NO_PRINT_2ND, o.longidx, o.arg, 0);
} else if (c == 316) { // --cs
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
if (o.arg == 0 || strcmp(o.arg, "short") == 0) {
opt.flag &= ~MM_F_OUT_CS_LONG;
} else if (strcmp(o.arg, "long") == 0) {
opt.flag |= MM_F_OUT_CS_LONG;
} else if (strcmp(o.arg, "none") == 0) {
opt.flag &= ~MM_F_OUT_CS;
} else if (mm_verbose >= 2) {
fprintf(stderr, "[WARNING]\033[1;31m --cs only takes 'short' or 'long'. Invalid values are assumed to be 'short'.\033[0m\n");
}
} else if (c == 319) { // --splice-flank
yes_or_no(&opt, MM_F_SPLICE_FLANK, o.longidx, o.arg, 1);
} else if (c == 324) { // --heap-sort
yes_or_no(&opt, MM_F_HEAP_SORT, o.longidx, o.arg, 1);
} else if (c == 326) { // --dual
yes_or_no(&opt, MM_F_NO_DUAL, o.longidx, o.arg, 0);
} else if (c == 'S') {
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
if (mm_verbose >= 2)
fprintf(stderr, "[WARNING]\033[1;31m option -S is deprecated and may be removed in future. Please use --cs=long instead.\033[0m\n");
} else if (c == 'V') {
puts(MM_VERSION);
return 0;
} else if (c == 'f') {
double x;
char *p;
x = strtod(o.arg, &p);
if (x < 1.0) opt.mid_occ_frac = x, opt.mid_occ = 0;
else opt.mid_occ = (int)(x + .499);
if (*p == ',') opt.max_occ = (int)(strtod(p+1, &p) + .499);
} else if (c == 'u') {
if (*o.arg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV; // both strands
else if (*o.arg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV; // match GT-AG
else if (*o.arg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR; // match CT-AC (reverse complement of GT-AG)
else if (*o.arg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV); // don't try to match the GT-AG signal
else {
fprintf(stderr, "[ERROR]\033[1;31m unrecognized cDNA direction\033[0m\n");
return 1;
}
} else if (c == 'z') {
opt.zdrop = opt.zdrop_inv = strtol(o.arg, &s, 10);
if (*s == ',') opt.zdrop_inv = strtol(s + 1, &s, 10);
} else if (c == 'O') {
opt.q = opt.q2 = strtol(o.arg, &s, 10);
if (*s == ',') opt.q2 = strtol(s + 1, &s, 10);
} else if (c == 'E') {
opt.e = opt.e2 = strtol(o.arg, &s, 10);
if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
}
}
if ((opt.flag & MM_F_SPLICE) && (opt.flag & MM_F_FRAG_MODE)) {
fprintf(stderr, "[ERROR]\033[1;31m --splice and --frag should not be specified at the same time.\033[0m\n");
return 1;
}
if (!fnw && !(opt.flag&MM_F_CIGAR))
ipt.flag |= MM_I_NO_SEQ;
if (mm_check_opt(&ipt, &opt) < 0)
return 1;
if (opt.best_n == 0) {
fprintf(stderr, "[WARNING]\033[1;31m changed '-N 0' to '-N %d --secondary=no'.\033[0m\n", old_best_n);
opt.best_n = old_best_n, opt.flag |= MM_F_NO_PRINT_2ND;
}
if (argc == o.ind || fp_help == stdout) {
fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");
fprintf(fp_help, "Options:\n");
fprintf(fp_help, " Indexing:\n");
fprintf(fp_help, " -H use homopolymer-compressed k-mer (preferrable for PacBio)\n");
fprintf(fp_help, " -k INT k-mer size (no larger than 28) [%d]\n", ipt.k);
fprintf(fp_help, " -w INT minimizer window size [%d]\n", ipt.w);
fprintf(fp_help, " -I NUM split index for every ~NUM input bases [4G]\n");
fprintf(fp_help, " -d FILE dump index to FILE []\n");
fprintf(fp_help, " Mapping:\n");
fprintf(fp_help, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac);
fprintf(fp_help, " -g NUM stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
fprintf(fp_help, " -G NUM max intron length (effective with -xsplice; changing -r) [200k]\n");
fprintf(fp_help, " -F NUM max fragment length (effective with -xsr or in the fragment mode) [800]\n");
fprintf(fp_help, " -r NUM bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw);
fprintf(fp_help, " -n INT minimal number of minimizers on a chain [%d]\n", opt.min_cnt);
fprintf(fp_help, " -m INT minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score);
// fprintf(fp_help, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy
fprintf(fp_help, " -X skip self and dual mappings (for the all-vs-all mode)\n");
fprintf(fp_help, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
fprintf(fp_help, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
fprintf(fp_help, " Alignment:\n");
fprintf(fp_help, " -A INT matching score [%d]\n", opt.a);
fprintf(fp_help, " -B INT mismatch penalty [%d]\n", opt.b);
fprintf(fp_help, " -O INT[,INT] gap open penalty [%d,%d]\n", opt.q, opt.q2);
fprintf(fp_help, " -E INT[,INT] gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [%d,%d]\n", opt.e, opt.e2);
fprintf(fp_help, " -z INT[,INT] Z-drop score and inversion Z-drop score [%d,%d]\n", opt.zdrop, opt.zdrop_inv);
fprintf(fp_help, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max);
fprintf(fp_help, " -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
fprintf(fp_help, " Input/Output:\n");
fprintf(fp_help, " -a output in the SAM format (PAF by default)\n");
fprintf(fp_help, " -o FILE output alignments to FILE [stdout]\n");
fprintf(fp_help, " -L write CIGAR with >65535 ops at the CG tag\n");
fprintf(fp_help, " -R STR SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n");
fprintf(fp_help, " -c output CIGAR in PAF\n");
fprintf(fp_help, " --cs[=STR] output the cs tag; STR is 'short' (if absent) or 'long' [none]\n");
fprintf(fp_help, " --MD output the MD tag\n");
fprintf(fp_help, " --eqx write =/X CIGAR operators\n");
fprintf(fp_help, " -Y use soft clipping for supplementary alignments\n");
fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads);
fprintf(fp_help, " -K NUM minibatch size for mapping [500M]\n");
// fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose);
fprintf(fp_help, " --version show version number\n");
fprintf(fp_help, " Preset:\n");
fprintf(fp_help, " -x STR preset (always applied before other options; see minimap2.1 for details) []\n");
fprintf(fp_help, " - map-pb/map-ont - PacBio/Nanopore vs reference mapping\n");
fprintf(fp_help, " - ava-pb/ava-ont - PacBio/Nanopore read overlap\n");
fprintf(fp_help, " - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
fprintf(fp_help, " - splice/splice:hq - long-read/Pacbio-CCS spliced alignment\n");
fprintf(fp_help, " - sr - genomic short-read mapping\n");
fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of these and other advanced command-line options.\n");
return fp_help == stdout? 0 : 1;
}
if ((opt.flag & MM_F_SR) && argc - o.ind > 3) {
fprintf(stderr, "[ERROR] incorrect input: in the sr mode, please specify no more than two query files.\n");
return 1;
}
preset_arg = (string)argv[o.ind] + "_" + preset_arg + "_minimizers_key_value_sorted";
idx_rdr = mm_idx_reader_open(argv[o.ind], &ipt, fnw);
total_time = __rdtsc();
if (idx_rdr == 0) {
fprintf(stderr, "[ERROR] failed to open file '%s': %s\n", argv[o.ind], strerror(errno));
return 1;
}
if (!idx_rdr->is_idx && fnw == 0 && argc - o.ind < 2) {
fprintf(stderr, "[ERROR] missing input: please specify a query file to map or option -d to keep the index\n");
mm_idx_reader_close(idx_rdr);
return 1;
}
if (opt.best_n == 0 && (opt.flag&MM_F_CIGAR) && mm_verbose >= 2)
fprintf(stderr, "[WARNING]\033[1;31m `-N 0' reduces alignment accuracy. Please use --secondary=no to suppress secondary alignments.\033[0m\n");
while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
int ret;
if ((opt.flag & MM_F_CIGAR) && (mi->flag & MM_I_NO_SEQ)) {
fprintf(stderr, "[ERROR] the prebuilt index doesn't contain sequences.\n");
mm_idx_destroy(mi);
mm_idx_reader_close(idx_rdr);
return 1;
}
if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
if (mm_idx_reader_eof(idx_rdr)) {
if (opt.split_prefix == 0)
ret = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
else
ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
} else {
ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
if (opt.split_prefix == 0 && mm_verbose >= 2)
fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.\033[0m\n");
}
if (ret != 0) {
mm_idx_destroy(mi);
mm_idx_reader_close(idx_rdr);
return 1;
}
}
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
if (argc != o.ind + 1) mm_mapopt_update(&opt, mi);
if (mm_verbose >= 3) mm_idx_stat(mi);
if(opt.L_hash == 1) {
fprintf(stderr, "Generating lisa-hash..\n");
mm_idx_dump_hash(preset_arg.c_str(), mi);
fprintf(stderr, "Lisa-hash saving done.. \n");
exit(0);
}
if (junc_bed) mm_idx_bed_read(mi, junc_bed, 1);
if (alt_list) mm_idx_alt_read(mi, alt_list);
ret = 0;
#ifdef LISA_HASH
fprintf(stderr, "Using LISA_HASH..\n");
mm_idx_destroy_mm_hash(mi);
char* prefix;
lh = new lisa_hash<uint64_t, uint64_t>(preset_arg, prefix);
fprintf(stderr, "Loading done.\n");
total_time = __rdtsc();
#endif
if (!(opt.flag & MM_F_FRAG_MODE)) {
for (i = o.ind + 1; i < argc; ++i) {
ret = mm_map_file(mi, argv[i], &opt, n_threads);
if (ret < 0) break;
}
} else {
ret = mm_map_file_frag(mi, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_threads);
}
if (ret < 0) {
fprintf(stderr, "ERROR: failed to map the query file\n");
exit(EXIT_FAILURE);
}
#ifdef LISA_HASH
mm_idx_destroy_seq(mi);
#else
mm_idx_destroy(mi);
#endif
}
n_parts = idx_rdr->n_parts;
mm_idx_reader_close(idx_rdr);
if (opt.split_prefix)
mm_split_merge(argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_parts);
if (fflush(stdout) == EOF) {
perror("[ERROR] failed to write the results");
exit(EXIT_FAILURE);
}
if (mm_verbose >= 3) {
fprintf(stderr, "[M::%s] Version: %s\n", __func__, MM_VERSION);
fprintf(stderr, "[M::%s] CMD:", __func__);
for (i = 0; i < argc; ++i)
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[M::%s] Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB\n", __func__, realtime() - mm_realtime0, cputime(), peakrss() / 1024.0 / 1024.0 / 1024.0);
}
#ifdef MANUAL_PROFILING
fprintf(stderr, "\n Number of reads = %lld Minimizer hit time = %lld dp_chaining time = %lld alignment time = %lld total time = %lld \n", num_reads, minimizer_hit_time, dp_chaining_time, alignment_time, __rdtsc() - total_time);
#endif
fprintf(stderr, "Total ticks: %lld \n",__rdtsc() - total_time);
#ifdef LISA_HASH
delete lh;
#endif
return 0;
}
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