File: main.c

package info (click to toggle)
miniasm 0.3%2Bdfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 632 kB
  • sloc: ansic: 2,528; perl: 120; sh: 66; makefile: 29
file content (211 lines) | stat: -rw-r--r-- 8,359 bytes parent folder | download | duplicates (3)
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
#include <unistd.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "kvec.h"
#include "sys.h"
#include "paf.h"
#include "sdict.h"
#include "miniasm.h"

#define MA_VERSION "0.3-r179"

static void print_subs(const sdict_t *d, const ma_sub_t *sub)
{
	uint32_t i;
	for (i = 0; i < d->n_seq; ++i)
		if (!d->seq[i].del && sub[i].s != sub[i].e)
			printf("%s\t%d\t%d\n", d->seq[i].name, sub[i].s, sub[i].e);
}

static void print_hits(size_t n_hits, const ma_hit_t *hit, const sdict_t *d, const ma_sub_t *sub)
{
	size_t i;
	for (i = 0; i < n_hits; ++i) {
		const ma_hit_t *p = &hit[i];
		const ma_sub_t *rq = &sub[p->qns>>32], *rt = &sub[p->tn];
		printf("%s:%d-%d\t%d\t%d\t%d\t%c\t%s:%d-%d\t%d\t%d\t%d\t%d\t%d\t255\n", d->seq[p->qns>>32].name, rq->s + 1, rq->e, rq->e - rq->s, (uint32_t)p->qns, p->qe,
				"+-"[p->rev], d->seq[p->tn].name, rt->s + 1, rt->e, rt->e - rt->s, p->ts, p->te, p->ml, p->bl);
	}
}

int main(int argc, char *argv[])
{
	ma_opt_t opt;
	int i, c, stage = 100, no_first = 0, no_second = 0, bi_dir = 1, o_set = 0, no_cont = 0;
	sdict_t *d, *excl = 0;
	ma_sub_t *sub = 0;
	ma_hit_t *hit;
	size_t n_hits;
	float cov = 40.0;
	char *fn_reads = 0, *outfmt = "ug";

	ma_opt_init(&opt);
	while ((c = getopt(argc, argv, "n:m:s:c:S:i:d:g:o:h:I:r:f:e:p:12VBRbF:")) >= 0) {
		if (c == 'm') opt.min_match = atoi(optarg);
		else if (c == 'i') opt.min_iden = atof(optarg);
		else if (c == 's') opt.min_span = atoi(optarg);
		else if (c == 'c') opt.min_dp = atoi(optarg);
		else if (c == 'o') opt.min_ovlp = atoi(optarg), o_set = 1;
		else if (c == 'S') stage = atoi(optarg);
		else if (c == 'd') opt.bub_dist = atoi(optarg);
		else if (c == 'g') opt.gap_fuzz = atoi(optarg);
		else if (c == 'h') opt.max_hang = atoi(optarg);
		else if (c == 'I') opt.int_frac = atof(optarg);
		else if (c == 'e') opt.max_ext = atoi(optarg);
		else if (c == 'f') fn_reads = optarg;
		else if (c == 'p') outfmt = optarg;
		else if (c == '1') no_first = 1;
		else if (c == '2') no_second = 1;
		else if (c == 'n') opt.n_rounds = atoi(optarg) - 1;
		else if (c == 'B') bi_dir = 1;
		else if (c == 'b') bi_dir = 0;
		else if (c == 'R') no_cont = 1;
		else if (c == 'F') opt.final_ovlp_drop_ratio = atof(optarg);
		else if (c == 'V') {
			printf("%s\n", MA_VERSION);
			return 0;
		} else if (c == 'r') {
			char *s;
			opt.max_ovlp_drop_ratio = strtod(optarg, &s);
			if (*s == ',') opt.min_ovlp_drop_ratio = strtod(s + 1, &s);
		}
	}
	if (o_set == 0) opt.min_ovlp = opt.min_span;
	if (argc == optind) {
		fprintf(stderr, "Usage: miniasm [options] <in.paf>\n");
		fprintf(stderr, "Options:\n");
		fprintf(stderr, "  Pre-selection:\n");
		fprintf(stderr, "    -R          prefilter clearly contained reads (2-pass required)\n");
		fprintf(stderr, "    -m INT      min match length [%d]\n", opt.min_match);
		fprintf(stderr, "    -i FLOAT    min identity [%.2g]\n", opt.min_iden);
		fprintf(stderr, "    -s INT      min span [%d]\n", opt.min_span);
		fprintf(stderr, "    -c INT      min coverage [%d]\n", opt.min_dp);
		fprintf(stderr, "  Overlap:\n");
		fprintf(stderr, "    -o INT      min overlap [same as -s]\n");
		fprintf(stderr, "    -h INT      max over hang length [%d]\n", opt.max_hang);
		fprintf(stderr, "    -I FLOAT    min end-to-end match ratio [%.2g]\n", opt.int_frac);
		fprintf(stderr, "  Layout:\n");
		fprintf(stderr, "    -g INT      max gap differences between reads for trans-reduction [%d]\n", opt.gap_fuzz);
		fprintf(stderr, "    -d INT      max distance for bubble popping [%d]\n", opt.bub_dist);
		fprintf(stderr, "    -e INT      small unitig threshold [%d]\n", opt.max_ext);
		fprintf(stderr, "    -f FILE     read sequences []\n");
		fprintf(stderr, "    -n INT      rounds of short overlap removal [%d]\n", opt.n_rounds + 1);
		fprintf(stderr, "    -r FLOAT[,FLOAT]\n");
		fprintf(stderr, "                max and min overlap drop ratio [%.2g,%.2g]\n", opt.max_ovlp_drop_ratio, opt.min_ovlp_drop_ratio);
		fprintf(stderr, "    -F FLOAT    aggressive overlap drop ratio in the end [%.2g]\n", opt.final_ovlp_drop_ratio);
		fprintf(stderr, "  Miscellaneous:\n");
		fprintf(stderr, "    -p STR      output information: bed, paf, sg or ug [%s]\n", outfmt);
//		fprintf(stderr, "    -B          only one direction of an arc is present in input PAF\n"); // deprecated; for backward compatibility
		fprintf(stderr, "    -b          both directions of an arc are present in input\n");
		fprintf(stderr, "    -1          skip 1-pass read selection\n");
		fprintf(stderr, "    -2          skip 2-pass read selection\n");
		fprintf(stderr, "    -V          print version number\n");
		fprintf(stderr, "\nSee miniasm.1 for detailed description of the command-line options.\n");
		return 1;
	}

	sys_init();
	d = sd_init();

	if (no_cont) {
		fprintf(stderr, "[M::%s] ===> Step 0: removing contained reads <===\n", __func__);
		excl = ma_hit_no_cont(argv[optind], opt.min_span, opt.min_match, opt.max_hang, opt.int_frac);
	}

	fprintf(stderr, "[M::%s] ===> Step 1: reading read mappings <===\n", __func__);
	hit = ma_hit_read(argv[optind], opt.min_span, opt.min_match, d, &n_hits, bi_dir, excl);

	if (!no_first) {
		fprintf(stderr, "[M::%s] ===> Step 2: 1-pass (crude) read selection <===\n", __func__);
		if (stage >= 2) {
			sub = ma_hit_sub(opt.min_dp, opt.min_iden, 0, n_hits, hit, d->n_seq);
			n_hits = ma_hit_cut(sub, opt.min_span, n_hits, hit);
		}
		if (stage >= 3) n_hits = ma_hit_flt(sub, opt.max_hang * 1.5, opt.min_ovlp * .5, n_hits, hit, &cov);
	}

	if (!no_second) {
		fprintf(stderr, "[M::%s] ===> Step 3: 2-pass (fine) read selection <===\n", __func__);
		if (stage >= 4) {
			ma_sub_t *sub2;
			sub2 = ma_hit_sub(opt.min_dp, opt.min_iden, opt.min_span/2, n_hits, hit, d->n_seq);
			n_hits = ma_hit_cut(sub2, opt.min_span, n_hits, hit);
			if (!no_first) {
				ma_sub_merge(d->n_seq, sub, sub2);
				free(sub2);
			} else {
				sub = sub2;
			}
		}
		if (stage >= 5) n_hits = ma_hit_contained(&opt, d, sub, n_hits, hit);
	}

	hit = (ma_hit_t*)realloc(hit, n_hits * sizeof(ma_hit_t));

	if (strcmp(outfmt, "bed") == 0) {
		print_subs(d, sub);
	} else if (strcmp(outfmt, "paf") == 0) {
		print_hits(n_hits, hit, d, sub);
	} else if (strcmp(outfmt, "ug") == 0 || strcmp(outfmt, "sg") == 0) {
		asg_t *sg = 0;
		ma_ug_t *ug = 0;

		fprintf(stderr, "[M::%s] ===> Step 4: graph cleaning <===\n", __func__);
		sg = ma_sg_gen(&opt, d, sub, n_hits, hit);
		if (stage >= 6) {
			fprintf(stderr, "[M::%s] ===> Step 4.1: transitive reduction <===\n", __func__);
			asg_arc_del_trans(sg, opt.gap_fuzz);
		}
		if (stage >= 7) {
			fprintf(stderr, "[M::%s] ===> Step 4.2: initial tip cutting and bubble popping <===\n", __func__);
			asg_cut_tip(sg, opt.max_ext);
			asg_pop_bubble(sg, opt.bub_dist);
		}
		if (stage >= 9) {
			fprintf(stderr, "[M::%s] ===> Step 4.3: cutting short overlaps (%d rounds in total) <===\n", __func__, opt.n_rounds + 1);
			for (i = 0; i <= opt.n_rounds; ++i) {
				float r = opt.min_ovlp_drop_ratio + (opt.max_ovlp_drop_ratio - opt.min_ovlp_drop_ratio) / opt.n_rounds * i;
				if (asg_arc_del_short(sg, r) != 0) {
					asg_cut_tip(sg, opt.max_ext);
					asg_pop_bubble(sg, opt.bub_dist);
				}
			}
		}
		if (stage >= 10) {
			fprintf(stderr, "[M::%s] ===> Step 4.4: removing short internal sequences and bi-loops <===\n", __func__);
			asg_cut_internal(sg, 1);
			asg_cut_biloop(sg, opt.max_ext);
			asg_cut_tip(sg, opt.max_ext);
			asg_pop_bubble(sg, opt.bub_dist);
		}
		if (stage >= 11) {
			fprintf(stderr, "[M::%s] ===> Step 4.5: aggressively cutting short overlaps <===\n", __func__);
			if (asg_arc_del_short(sg, opt.final_ovlp_drop_ratio) != 0) {
				asg_cut_tip(sg, opt.max_ext);
				asg_pop_bubble(sg, opt.bub_dist);
			}
		}

		if (strcmp(outfmt, "ug") == 0) {
			fprintf(stderr, "[M::%s] ===> Step 5: generating unitigs <===\n", __func__);
			ug = ma_ug_gen(sg);
			if (fn_reads) ma_ug_seq(ug, d, sub, fn_reads);
			ma_ug_print(ug, d, sub, stdout);
		} else ma_sg_print(sg, d, sub, stdout);

		asg_destroy(sg);
		ma_ug_destroy(ug);
	}

	free(sub); free(hit);
	sd_destroy(d);
	if (excl) sd_destroy(excl);

	fprintf(stderr, "[M::%s] Version: %s\n", __func__, MA_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\n", __func__, sys_realtime(), sys_cputime());
	return 0;
}