fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-03 00:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

mm2-fast: Initial commit

Browse Source
This commit is contained in:
Saurabh
2021-06-16 15:50:17 -04:00
committed by Heng Li
parent b6ff332de1
commit 0369874d4e
13 changed files with 1353 additions and 50 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+79 -3
View File
@@ -1,13 +1,54 @@
/* 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>
@@ -108,11 +149,12 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
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:";
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;
@@ -122,9 +164,11 @@ int main(int argc, char *argv[])
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;
@@ -141,6 +185,7 @@ int main(int argc, char *argv[])
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
@@ -345,7 +390,12 @@ int main(int argc, char *argv[])
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;
@@ -387,9 +437,23 @@ int main(int argc, char *argv[])
__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);
@@ -398,11 +462,15 @@ int main(int argc, char *argv[])
} else {
ret = mm_map_file_frag(mi, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_threads);
}
mm_idx_destroy(mi);
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);
@@ -422,5 +490,13 @@ int main(int argc, char *argv[])
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);
}
return 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;
}