r287: refined CLI options and manpage
This commit is contained in:
Heng Li
parent
0f4c823b0c
commit
d240318741
8
align.c
8
align.c
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@ -135,7 +135,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
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for (i = 0; i < tlen; ++i) fputc("ACGTN"[tseq[i]], stderr); fputc('\n', stderr);
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for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr); fputc('\n', stderr);
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}
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if (opt->flag & MM_F_CDNA)
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if (opt->flag & MM_F_SPLICE)
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ksw_extd2_noins_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, 0, -1, opt->zdrop, flag, ez);
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else if (opt->q == opt->q2 && opt->e == opt->e2)
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ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, opt->zdrop, flag, ez);
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@ -259,7 +259,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
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bw = (int)(opt->bw * 1.5 + 1.);
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r2->cnt = 0;
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if (!(opt->flag & MM_F_CDNA))
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if (!(opt->flag & MM_F_SPLICE))
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mm_fix_bad_ends(r, a, opt->bw, &as1, &cnt1);
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else as1 = r->as, cnt1 = r->cnt;
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mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
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@ -362,7 +362,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
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assert(re1 - rs1 <= re0 - rs0);
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if (r->p) {
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mm_idx_getseq(mi, rid, rs1, re1, tseq);
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mm_update_extra(r->p, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e, (opt->flag&MM_F_CDNA)? opt->q2 : 0);
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mm_update_extra(r->p, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e, (opt->flag&MM_F_SPLICE)? opt->q2 : 0);
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}
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kfree(km, tseq);
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@ -403,7 +403,7 @@ static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, i
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if (ez->n_cigar == 0) goto end_align1_inv; // should never be here
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mm_append_cigar(r_inv, ez->n_cigar, ez->cigar);
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r_inv->p->dp_score = ez->max;
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mm_update_extra(r_inv->p, qseq + q_off, tseq + t_off, mat, opt->q, opt->e, (opt->flag&MM_F_CDNA)? opt->q2 : 0);
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mm_update_extra(r_inv->p, qseq + q_off, tseq + t_off, mat, opt->q, opt->e, (opt->flag&MM_F_SPLICE)? opt->q2 : 0);
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r_inv->id = -1;
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r_inv->parent = MM_PARENT_UNSET;
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r_inv->inv = 1;
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43
main.c
43
main.c
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@ -8,7 +8,7 @@
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#include "minimap.h"
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#include "mmpriv.h"
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#define MM_VERSION "2.0-r286-dirty"
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#define MM_VERSION "2.0-r287-dirty"
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void liftrlimit()
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{
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@ -31,6 +31,8 @@ static struct option long_options[] = {
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{ "max-chain-skip", required_argument, 0, 0 },
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{ "min-dp-len", required_argument, 0, 0 },
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{ "print-aln-seq", no_argument, 0, 0 },
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{ "splice", no_argument, 0, 0 },
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{ "max-intron-len", required_argument, 0, 'G' },
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{ "version", no_argument, 0, 'V' },
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{ "min-count", required_argument, 0, 'n' },
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{ "min-chain-score",required_argument, 0, 'm' },
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@ -40,10 +42,21 @@ static struct option long_options[] = {
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{ 0, 0, 0, 0}
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};
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static inline int64_t mm_parse_num(const char *str)
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{
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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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return (int64_t)(x + .499);
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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 = 15, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx, idx_par_set = 0;
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int i, c, k = 15, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx, idx_par_set = 0, max_intron_len = 0;
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int minibatch_size = 200000000;
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uint64_t batch_size = 4000000000ULL;
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mm_bseq_file_t *fp = 0;
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@ -59,12 +72,12 @@ int main(int argc, char *argv[])
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else if (c == 'k') k = atoi(optarg), idx_par_set = 1;
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else if (c == 'H') is_hpc = 1, idx_par_set = 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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else if (c == 'r') opt.bw = (int)mm_parse_num(optarg);
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else if (c == 'f') opt.mid_occ_frac = atof(optarg);
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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 == 'G') opt.max_gap_ref = atoi(optarg);
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else if (c == 'g') opt.max_gap = (int)mm_parse_num(optarg);
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else if (c == 'G') max_intron_len = (int)mm_parse_num(optarg);
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else if (c == 'N') opt.best_n = atoi(optarg);
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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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@ -80,6 +93,8 @@ int main(int argc, char *argv[])
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else if (c == 'B') opt.b = atoi(optarg);
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else if (c == 'z') opt.zdrop = atoi(optarg);
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else if (c == 's') opt.min_dp_max = atoi(optarg);
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else if (c == 'I') batch_size = mm_parse_num(optarg);
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else if (c == 'K') minibatch_size = (int)mm_parse_num(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 == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
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@ -89,6 +104,7 @@ int main(int argc, char *argv[])
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else if (c == 0 && long_idx == 7) opt.max_chain_skip = atoi(optarg); // --max-chain-skip
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else if (c == 0 && long_idx == 8) opt.min_ksw_len = atoi(optarg); // --min-dp-len
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else if (c == 0 && long_idx == 9) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ; // --print-aln-seq
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else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice
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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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@ -98,15 +114,6 @@ int main(int argc, char *argv[])
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} else if (c == 'E') {
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opt.e = opt.e2 = strtol(optarg, &s, 10);
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if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
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} else if (c == 'I' || c == 'K') {
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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 == '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 == 'x') {
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if (strcmp(optarg, "ava-ont") == 0) {
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opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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@ -130,9 +137,9 @@ int main(int argc, char *argv[])
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k = 19, w = 19;
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opt.a = 1, opt.b = 9, opt.q = 16, opt.q2 = 41, opt.e = 2, opt.e2 = 1, opt.zdrop = 200;
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opt.min_dp_max = 200;
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} else if (strcmp(optarg, "cdna") == 0) {
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} else if (strcmp(optarg, "splice") == 0 || strcmp(optarg, "cdna") == 0) {
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k = 15, w = 5;
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opt.flag |= MM_F_CDNA;
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opt.flag |= MM_F_SPLICE;
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opt.max_gap = 2000, opt.max_gap_ref = opt.bw = 100000;
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opt.a = 1, opt.b = 2, opt.q = 2, opt.e = 1, opt.q2 = 32, opt.e2 = 0;
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opt.zdrop = 200;
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@ -143,6 +150,8 @@ int main(int argc, char *argv[])
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}
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}
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if (w < 0) w = (int)(.6666667 * k + .499);
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if ((opt.flag & MM_F_SPLICE) && max_intron_len > 0)
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opt.max_gap_ref = opt.bw = max_intron_len;
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if (argc == optind) {
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fprintf(stderr, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");
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@ -163,6 +172,7 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -X skip self and dual mappings (for the all-vs-all mode)\n");
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fprintf(stderr, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
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fprintf(stderr, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
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fprintf(stderr, " -G NUM max intron length (only effective following -x splice) [100k]\n");
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fprintf(stderr, " Alignment:\n");
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fprintf(stderr, " -A INT matching score [%d]\n", opt.a);
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fprintf(stderr, " -B INT mismatch penalty [%d]\n", opt.b);
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@ -187,6 +197,7 @@ int main(int argc, char *argv[])
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fprintf(stderr, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n");
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fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
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fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n");
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fprintf(stderr, " splice: -k15 -w5 --splice -g2000 -G100k -A1 -B2 -O2,32 -E1,0 -z200 (long-read spliced aln)\n");
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fprintf(stderr, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");
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return 1;
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}
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6
map.c
6
map.c
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@ -245,7 +245,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
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i == 0? 0 : ((int32_t)a[i].y - (int32_t)a[i-1].y) - ((int32_t)a[i].x - (int32_t)a[i-1].x));
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max_gap_ref = opt->max_gap_ref >= 0? opt->max_gap_ref : opt->max_gap;
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n_u = mm_chain_dp(max_gap_ref, opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, !!(opt->flag&MM_F_CDNA), n_a, a, &u, b->km);
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n_u = mm_chain_dp(max_gap_ref, opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, !!(opt->flag&MM_F_SPLICE), n_a, a, &u, b->km);
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regs = mm_gen_regs(b->km, qlen, n_u, u, a);
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*n_regs = n_u;
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@ -258,7 +258,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
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if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
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mm_set_parent(b->km, opt->mask_level, *n_regs, regs);
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mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
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if (!(opt->flag & MM_F_CDNA))
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if (!(opt->flag & MM_F_SPLICE))
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mm_join_long(b->km, opt, qlen, n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
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}
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if (opt->flag & MM_F_CIGAR) {
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@ -347,7 +347,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
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int intron_thres = -1;
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for (i = 0; i < p->n_threads; ++i) mm_tbuf_destroy(s->buf[i]);
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free(s->buf);
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if (p->opt->flag & MM_F_CDNA)
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if (p->opt->flag & MM_F_SPLICE)
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intron_thres = mm_min_intron_len(p->opt->q, p->opt->e, p->opt->q2);
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if ((p->opt->flag & MM_F_OUT_CS) && !(mm_dbg_flag & MM_DBG_NO_KALLOC)) km = km_init();
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for (i = 0; i < s->n_seq; ++i) {
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@ -14,7 +14,7 @@
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#define MM_F_NO_QUAL 0x10
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#define MM_F_OUT_CG 0x20
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#define MM_F_OUT_CS 0x40
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#define MM_F_CDNA 0x80
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#define MM_F_SPLICE 0x80
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#define MM_IDX_MAGIC "MMI\2"
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28
minimap2.1
28
minimap2.1
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@ -162,6 +162,12 @@ secondary alignments [5]. This option has no effect when
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.B -X
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is applied.
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.TP
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.BI -G \ NUM
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Maximal intron length in the splice mode. This option also changes the
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bandwidth to
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.IR NUM .
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Increasing this option slows down spliced alignment.
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.TP
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.BI --max-chain-skip \ INT
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A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming
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for chaining. The time complexity is quadratic in the number of seeds. This
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@ -277,13 +283,13 @@ Long assembly to reference mapping
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.B -w19 -A1 -B9 -O16,41 -E2,1 -s200
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.BR -z200 ).
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Up to 10% sequence divergence.
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.TP 8
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.TP
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.B ava-pb
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PacBio all-vs-all overlap mapping
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.RB ( -Hk19
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.B -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip
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.BR 25 ).
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.TP 8
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.TP
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.B ava-ont
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Oxford Nanopore all-vs-all overlap mapping
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.RB ( -k15
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@ -292,6 +298,20 @@ Oxford Nanopore all-vs-all overlap mapping
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Similarly, the major difference from
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.B ava-pb
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is that this preset is not using HPC minimizers.
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.TP
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.B splice
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Long-read spliced alignment
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.RB ( -k15
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.B -w5 --splice -g2000 -G100k -A1 -B2 -O2,32 -E1,0
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.BR -z200 ).
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As of now, minimap2 only finds approximate exon boundaries. The true boundaries
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are usually within 10bp around the reported positions. In the splice mode,
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1) long deletions are taken as introns and represented as the
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.RB ` N '
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CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap
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costs are different during chaining; 4) the computation of the
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.RB ` ms '
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tag ignores introns to demote hits to pseudogenes.
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.RE
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.SS Miscellaneous options
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.TP 10
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@ -367,6 +387,10 @@ Minimap2 does not work well with Illumina short reads as of now.
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*
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Minimap2 requires SSE2 instructions to compile. It is possible to add
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non-SSE2 support, but it would make minimap2 slower by several times.
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.TP
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*
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In the splice mode, minimap2 is unable to find the precise exon boundaries.
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The true bounraries are usually within 10bp around the reported locations.
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.SH SEE ALSO
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.PP
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miniasm(1), minimap(1), bwa(1).
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