use long options
This commit is contained in:
Heng Li
parent
640b1a1727
commit
4b8e88a5f4
5
format.c
5
format.c
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@ -57,7 +57,10 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
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void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r)
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{
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s->l = 0;
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mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t%s\t%d\t%d\t%d", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev], mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re);
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mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
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if (mi->seq[r->rid].name) mm_sprintf_lite(s, "%s", mi->seq[r->rid].name);
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else mm_sprintf_lite(s, "%d", r->rid);
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mm_sprintf_lite(s, "\t%d\t%d\t%d", mi->seq[r->rid].len, r->rs, r->re);
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if (r->p) mm_sprintf_lite(s, "\t%d\t%d", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
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else mm_sprintf_lite(s, "\t%d\t%d", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
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mm_sprintf_lite(s, "\t%d\tcm:i:%d", r->mapq, r->cnt);
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34
main.c
34
main.c
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@ -1,4 +1,4 @@
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#include <unistd.h>
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#include <getopt.h>
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#include <stdlib.h>
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#include <stdio.h>
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#include <string.h>
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@ -40,11 +40,18 @@ static int test_idx(const char *fn)
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return is_idx;
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}
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static struct option long_options[] = {
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{ "bucket-bits", required_argument, 0, 0 },
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{ "mb-size", required_argument, 0, 0 },
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{ "int-rname", no_argument, 0, 0 },
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{ 0, 0, 0, 0}
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};
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int main(int argc, char *argv[])
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{
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mm_mapopt_t opt;
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int i, c, k = 17, w = -1, b = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0;
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int mini_batch_size = 100000000;
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int i, c, k = 17, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx;
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int minibatch_size = 100000000;
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uint64_t batch_size = 4000000000ULL;
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bseq_file_t *fp = 0;
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char *fnw = 0;
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@ -54,10 +61,9 @@ int main(int argc, char *argv[])
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mm_realtime0 = realtime();
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mm_mapopt_init(&opt);
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while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hcp:m:z:F:")) >= 0) {
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while ((c = getopt_long(argc, argv, "w:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:m:z:F:", long_options, &long_idx)) >= 0) {
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if (c == 'w') w = atoi(optarg);
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else if (c == 'k') k = atoi(optarg);
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else if (c == 'b') b = atoi(optarg);
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else if (c == 'H') is_hpc = 1;
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else if (c == 'd') fnw = optarg; // the above are indexing related options, except -I
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else if (c == 'r') opt.bw = atoi(optarg);
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@ -65,27 +71,27 @@ int main(int argc, char *argv[])
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else if (c == 't') n_threads = atoi(optarg);
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else if (c == 'v') mm_verbose = atoi(optarg);
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else if (c == 'g') opt.max_gap = atoi(optarg);
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else if (c == 'N') keep_name = 0;
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else if (c == 'p') opt.pri_ratio = atof(optarg);
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else if (c == 'm') opt.mask_level = atof(optarg);
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else if (c == 'c') opt.flag |= MM_F_CIGAR;
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else if (c == 'D') opt.flag |= MM_F_NO_SELF;
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else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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else if (c == 'T') opt.sdust_thres = atoi(optarg);
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else if (c == 's') opt.min_score = atoi(optarg);
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else if (c == 'z') opt.zdrop = atoi(optarg);
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else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // bucket-bits
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else if (c == 0 && long_idx == 2) keep_name = 0; // int-rname
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else if (c == 'V') {
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puts(MM_VERSION);
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return 0;
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} else if (c == 'B' || c == 'I') {
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} else if (c == 'I' || (c == 0 && long_idx == 1)) {
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double x;
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char *p;
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x = strtod(optarg, &p);
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if (*p == 'G' || *p == 'g') x *= 1e9;
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else if (*p == 'M' || *p == 'm') x *= 1e6;
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else if (*p == 'K' || *p == 'k') x *= 1e3;
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if (c == 'B') mini_batch_size = (uint64_t)(x + .499);
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else batch_size = (uint64_t)(x + .499);
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if (c == 'I') batch_size = (uint64_t)(x + .499);
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else minibatch_size = (uint64_t)(x + .499);
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} else if (c == 'F') {
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if (strcmp(optarg, "sam") == 0) opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
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else if (strcmp(optarg, "paf") == 0) opt.flag &= ~MM_F_OUT_SAM;
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@ -112,14 +118,12 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -w INT minizer window size [{-k}*2/3]\n");
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fprintf(stderr, " -I NUM split index for every ~NUM input bases [4G]\n");
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fprintf(stderr, " -d FILE dump index to FILE []\n");
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// fprintf(stderr, " -b INT bucket bits [%d]\n", b); // most users wouldn't care about this
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fprintf(stderr, " Mapping:\n");
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fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", opt.mid_occ_frac);
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fprintf(stderr, " -r INT bandwidth [%d]\n", opt.bw);
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fprintf(stderr, " -s INT min score [%d]\n", opt.min_score);
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fprintf(stderr, " -g INT split a mapping if there is a gap longer than INT [%d]\n", opt.max_gap);
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fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres);
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// fprintf(stderr, " -D skip self mappings but keep dual mappings\n"); // too confusing to expose to end users
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fprintf(stderr, " -S skip self and dual mappings\n");
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fprintf(stderr, " -p FLOAT threshold to output a mapping [%g]\n", opt.pri_ratio);
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fprintf(stderr, " -z INT Z-drop score [%d]\n", opt.zdrop);
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@ -129,9 +133,7 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -F STR output format: sam or paf [paf]\n");
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fprintf(stderr, " -c output CIGAR in PAF\n");
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fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
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// fprintf(stderr, " -B NUM process ~NUM bp in each mini-batch [100M]\n");
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// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);
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// fprintf(stderr, " -N use integer as target names\n");
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fprintf(stderr, " -V show version number\n");
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fprintf(stderr, "\nSee minimap2.1 for detailed description of the command-line options.\n");
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return 1;
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@ -149,7 +151,7 @@ int main(int argc, char *argv[])
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mm_idx_t *mi = 0;
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if (fpr) mi = mm_idx_load(fpr);
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else if (!bseq_eof(fp))
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mi = mm_idx_gen(fp, w, k, b, is_hpc, mini_batch_size, n_threads, batch_size, keep_name);
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mi = mm_idx_gen(fp, w, k, bucket_bits, is_hpc, minibatch_size, n_threads, batch_size, keep_name);
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if (mi == 0) break;
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if (mm_verbose >= 3)
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fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
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@ -162,7 +164,7 @@ int main(int argc, char *argv[])
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if (argc != optind + 1) mm_mapopt_update(&opt, mi);
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if (mm_verbose >= 3) mm_idx_stat(mi);
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for (i = optind + 1; i < argc; ++i)
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mm_map_file(mi, argv[i], &opt, n_threads, mini_batch_size);
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mm_map_file(mi, argv[i], &opt, n_threads, minibatch_size);
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mm_idx_destroy(mi);
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}
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if (fpw) fclose(fpw);
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