ruby-minigraph 0.0.20.0

data/ext/minigraph/main.c

@@ -0,0 +1,301 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include "mgpriv.h"
+#include "gfa-priv.h"
+#include "sys.h"
+#include "ketopt.h"
+
+#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[] = {
+	{ "version",      ko_no_argument,       300 },
+	{ "vc",           ko_no_argument,       301 },
+	{ "secondary",    ko_required_argument, 302 },
+	{ "ins-qovlp",    ko_required_argument, 303 },
+	{ "heap-sort",    ko_required_argument, 304 },
+	{ "show-unmap",   ko_required_argument, 305 },
+	{ "ggen",         ko_optional_argument, 306 },
+	{ "rmq",          ko_optional_argument, 307 },
+	{ "gg-min-end-cnt",  ko_required_argument, 309 },
+	{ "gg-min-end-frac", ko_required_argument, 310 },
+	{ "no-comp-path", ko_no_argument,       312 },
+	{ "gg-match-pen", ko_required_argument, 313 },
+	{ "frag",         ko_no_argument,       314 },
+	{ "cov",          ko_no_argument,       315 },
+	{ "min-cov-blen", ko_required_argument, 316 },
+	{ "min-cov-mapq", ko_required_argument, 317 },
+	{ "gap-pen",      ko_required_argument, 318 },
+	{ "ref-bonus",    ko_required_argument, 319 },
+	{ "max-gap-pre",  ko_required_argument, 320 },
+	{ "max-lc-skip",  ko_required_argument, 321 },
+	{ "max-gc-skip",  ko_required_argument, 322 },
+	{ "max-lc-iter",  ko_required_argument, 323 },
+	{ "max-rmq-size", ko_required_argument, 324 },
+	{ "inv",          ko_required_argument, 325 },
+	{ "write-mz",     ko_no_argument,       326 },
+	{ "call",         ko_no_argument,       327 },
+	{ "cap-calloc",   ko_required_argument, 328 },
+	{ "gdp-max-ed",   ko_required_argument, 329 },
+	{ "no-kalloc",    ko_no_argument,       401 },
+	{ "dbg-qname",    ko_no_argument,       402 },
+	{ "dbg-lchain",   ko_no_argument,       403 },
+	{ "dbg-insert",   ko_no_argument,       404 },
+	{ "dbg-shortk",   ko_no_argument,       405 },
+	{ "dbg-gc1",      ko_no_argument,       406 },
+	{ "dbg-lc-prof",  ko_no_argument,       407 },
+	{ "dbg-mwf-long", ko_no_argument,       408 },
+	{ "dbg-mwf-seq",  ko_no_argument,       409 },
+	{ 0, 0, 0 }
+};
+
+static inline int64_t mm_parse_num2(const char *str, char **q)
+{
+	double x;
+	char *p;
+	x = strtod(str, &p);
+	if (*p == 'G' || *p == 'g') x *= 1e9, ++p;
+	else if (*p == 'M' || *p == 'm') x *= 1e6, ++p;
+	else if (*p == 'K' || *p == 'k') x *= 1e3, ++p;
+	if (q) *q = p;
+	return (int64_t)(x + .499);
+}
+
+static inline int64_t mm_parse_num(const char *str)
+{
+	return mm_parse_num2(str, 0);
+}
+
+static inline void yes_or_no(uint64_t *flag_, uint64_t f, int long_idx, const char *arg, int yes_to_set)
+{
+	uint64_t flag = *flag_;
+	if (yes_to_set) {
+		if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) flag |= f;
+		else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) flag &= ~f;
+		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) flag &= ~f;
+		else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) flag |= f;
+		else fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
+	}
+	*flag_ = flag;
+}
+
+int main(int argc, char *argv[])
+{
+	const char *opt_str = "x:k:w:t:r:m:n:g:K:o:p:N:Pq:d:l:f:U:M:F:j:L:DSc";
+	ketopt_t o = KETOPT_INIT;
+	mg_mapopt_t opt;
+	mg_idxopt_t ipt;
+	mg_ggopt_t gpt;
+	int i, c, ret, n_threads = 4;
+	char *s;
+	FILE *fp_help = stderr;
+	gfa_t *g;
+
+	mg_verbose = 3;
+	liftrlimit();
+	mg_realtime0 = realtime();
+	mg_opt_set(0, &ipt, &opt, &gpt);
+
+	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') {
+			if (mg_opt_set(o.arg, &ipt, &opt, &gpt) < 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 == 'k') ipt.k = atoi(o.arg);
+		else if (c == 't') n_threads = atoi(o.arg);
+		else if (c == 'f') opt.occ_max1_frac = atof(o.arg);
+		else if (c == 'g') opt.max_gap = mm_parse_num(o.arg);
+		else if (c == 'F') opt.max_frag_len = mm_parse_num(o.arg);
+		else if (c == 'K') opt.mini_batch_size = mm_parse_num(o.arg);
+		else if (c == 'p') opt.pri_ratio = atof(o.arg);
+		else if (c == 'N') opt.best_n = mm_parse_num(o.arg);
+		else if (c == 'P') opt.flag |= MG_M_ALL_CHAINS;
+		else if (c == 'D') opt.flag |= MG_M_NO_DIAG;
+		else if (c == 'M') opt.mask_level = atof(o.arg);
+		else if (c == 'j') opt.div = atof(o.arg);
+		else if (c == 'l') gpt.min_map_len = mm_parse_num(o.arg);
+		else if (c == 'd') gpt.min_depth_len = mm_parse_num(o.arg);
+		else if (c == 'q') gpt.min_mapq = atoi(o.arg);
+		else if (c == 'L') gpt.min_var_len = atoi(o.arg);
+		else if (c == 'S') opt.flag |= MG_M_WRITE_LCHAIN;
+		else if (c == 'c') opt.flag |= MG_M_CIGAR;
+		else if (c == 301) opt.flag |= MG_M_VERTEX_COOR;      // --vc
+		else if (c == 309) gpt.ggs_min_end_cnt = atoi(o.arg);  // --gg-min-end-cnt
+		else if (c == 310) gpt.ggs_min_end_frac = atof(o.arg); // --gg-min-end-frac
+		else if (c == 312) opt.flag |= MG_M_NO_COMP_PATH;     // --no-comp-path
+		else if (c == 313) gpt.match_pen = atoi(o.arg);       // --gg-match-pen
+		else if (c == 314) opt.flag |= MG_M_FRAG_MODE | MG_M_FRAG_MERGE;       // --frag
+		else if (c == 315) opt.flag |= MG_M_CAL_COV | MG_M_SKIP_GCHECK, gpt.flag |= MG_G_CAL_COV; // --cov
+		else if (c == 316) opt.min_cov_blen = mm_parse_num(o.arg);             // --min-cov-blen
+		else if (c == 317) opt.min_cov_mapq = atoi(o.arg);                     // --min-cov-mapq
+		else if (c == 318) opt.chn_pen_gap = atof(o.arg);     // --gap-pen
+		else if (c == 319) opt.ref_bonus = atoi(o.arg);       // --ref-bonus
+		else if (c == 320) opt.max_gap_pre = mm_parse_num(o.arg); // --max-gap-pre
+		else if (c == 321) opt.max_lc_skip = atoi(o.arg);     // --max-lc-skip
+		else if (c == 322) opt.max_gc_skip = atoi(o.arg);     // --max-gc-skip
+		else if (c == 323) opt.max_lc_iter = mm_parse_num(o.arg);  // --max-lc-iter
+		else if (c == 324) opt.rmq_size_cap = mm_parse_num(o.arg); // --max-rmq-size
+		else if (c == 326) opt.flag |= MG_M_WRITE_MZ | MG_M_WRITE_LCHAIN; // --write-mz
+		else if (c == 327) gpt.flag |= MG_G_CALL, opt.flag |= MG_M_SKIP_GCHECK; // --call
+		else if (c == 328) opt.cap_kalloc = mm_parse_num(o.arg); // --cap-kalloc
+		else if (c == 329) opt.gdp_max_ed = mm_parse_num(o.arg); // --gdp-max-ed
+		else if (c == 401) mg_dbg_flag |= MG_DBG_NO_KALLOC;   // --no-kalloc
+		else if (c == 402) mg_dbg_flag |= MG_DBG_QNAME;       // --dbg-qname
+		else if (c == 403) mg_dbg_flag |= MG_DBG_LCHAIN;      // --dbg-lchain
+		else if (c == 404) mg_dbg_flag |= MG_DBG_INSERT;      // --dbg-insert
+		else if (c == 405) mg_dbg_flag |= MG_DBG_SHORTK;      // --dbg-shortk
+		else if (c == 406) mg_dbg_flag |= MG_DBG_GC1;         // --dbg-gc1
+		else if (c == 407) mg_dbg_flag |= MG_DBG_LC_PROF;     // --dbg-lc-prof
+		else if (c == 408) mg_dbg_flag |= MG_DBG_MINIWFA;     // --dbg-mwf-long
+		else if (c == 409) mg_dbg_flag |= MG_DBG_MWF_SEQ;     // --dbg-mwf-seq
+		else if (c == 'U') {
+			opt.occ_max1 = (int)mm_parse_num2(o.arg, &s);
+			if (*s == ',') opt.occ_max1_cap = (int)mm_parse_num2(s + 1, &s);
+		} else if (c == 'r') {
+			opt.bw = (int)mm_parse_num2(o.arg, &s);
+			if (*s == ',') opt.bw_long = (int)mm_parse_num2(s + 1, &s);
+		} else if (c == 'n') {
+			opt.min_gc_cnt = (int)mm_parse_num2(o.arg, &s);
+			if (*s == ',') opt.min_lc_cnt = (int)mm_parse_num2(s + 1, &s);
+		} else if (c == 'm') {
+			opt.min_gc_score = (int)mm_parse_num2(o.arg, &s);
+			if (*s == ',') opt.min_lc_score = (int)mm_parse_num2(s + 1, &s);
+		} 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\n", o.arg);
+					exit(1);
+				}
+			}
+		} else if (c == 306) { // --ggen
+			if (o.arg) {
+				if (strcmp(o.arg, "none") == 0) gpt.algo = MG_G_NONE;
+				else if (strcmp(o.arg, "simple") == 0) gpt.algo = MG_G_GGSIMPLE;
+				else {
+					fprintf(stderr, "ERROR: unknown graph generation algorithm \"%s\"\n", o.arg);
+					return 1;
+				}
+			} else gpt.algo = MG_G_GGSIMPLE;
+		} else if (c == 302) { // --secondary
+			yes_or_no(&opt.flag, MG_M_PRINT_2ND, o.longidx, o.arg, 1);
+		} else if (c == 303) { // --ins-qovlp
+			yes_or_no(&gpt.flag, MG_G_NO_QOVLP, o.longidx, o.arg, 1);
+		} else if (c == 304) { // --heap-sort
+			yes_or_no(&opt.flag, MG_M_HEAP_SORT, o.longidx, o.arg, 1);
+		} else if (c == 305) { // --show-unmap
+			yes_or_no(&opt.flag, MG_M_SHOW_UNMAP, o.longidx, o.arg, 1);
+		} else if (c == 307) { // --rmq
+			yes_or_no(&opt.flag, MG_M_RMQ, o.longidx, o.arg, 1);
+		} else if (c == 325) { // --inv
+			yes_or_no(&gpt.flag, MG_G_NO_INV, o.longidx, o.arg, 0);
+		} else if (c == 300) { // --version
+			puts(MG_VERSION);
+			return 0;
+		}
+	}
+	if (mg_opt_check(&ipt, &opt, &gpt) < 0)
+		return 1;
+	if (gpt.algo == MG_G_GGSIMPLE && !(opt.flag&MG_M_CIGAR))
+		fprintf(stderr, "[WARNING]\033[1;31m it is recommended to add -c for graph generation\033[0m\n");
+
+	if (argc == o.ind || fp_help == stdout) {
+		fprintf(fp_help, "Usage: minigraph [options] <target.gfa> <query.fa> [...]\n");
+		fprintf(fp_help, "Options:\n");
+		fprintf(fp_help, "  Indexing:\n");
+		fprintf(fp_help, "    -k INT       k-mer size (no larger than 28) [%d]\n", ipt.k);
+		fprintf(fp_help, "    -w INT       minizer window size [%d]\n", ipt.w);
+		fprintf(fp_help, "  Mapping:\n");
+		fprintf(fp_help, "    -c           perform base alignment; RECOMMENDED\n");
+		fprintf(fp_help, "    -f FLOAT     ignore top FLOAT fraction of repetitive minimizers [%g]\n", opt.occ_max1_frac);
+		fprintf(fp_help, "    -U INT[,INT] choose the minimizer occurrence threshold within this interval [%d,%d]\n", opt.occ_max1, opt.occ_max1_cap);
+		fprintf(fp_help, "    -j FLOAT     expected sequence divergence [%g]\n", opt.div);
+		fprintf(fp_help, "    -g NUM       stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
+		fprintf(fp_help, "    -F NUM       max fragment length (effective with -xsr or in the fragment mode) [%d]\n", opt.max_frag_len);
+		fprintf(fp_help, "    -r NUM[,NUM] bandwidth for the two rounds of chaining [%d,%d]\n", opt.bw, opt.bw_long);
+		fprintf(fp_help, "    -n INT[,INT] minimal number of minimizers on a graph/linear chain [%d,%d]\n", opt.min_gc_cnt, opt.min_lc_cnt);
+		fprintf(fp_help, "    -m INT[,INT] minimal graph/linear chaining score [%d,%d]\n", opt.min_gc_score, opt.min_lc_score);
+		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 mappings [%d]\n", opt.best_n);
+		fprintf(fp_help, "    -D           skip self diagonal matches\n");
+		fprintf(fp_help, "  Graph generation:\n");
+		fprintf(fp_help, "    --ggen       perform incremental graph generation\n");
+		fprintf(fp_help, "    -q INT       min mapping quality [%d]\n", gpt.min_mapq);
+		fprintf(fp_help, "    -l NUM       min alignment length [%d]\n", gpt.min_map_len);
+		fprintf(fp_help, "    -d NUM       min alignment length for depth calculation [%d]\n", gpt.min_depth_len);
+		fprintf(fp_help, "    -L INT       min variant length [%d]\n", gpt.min_var_len);
+		fprintf(fp_help, "    --call       call the graph path in each bubble and output BED\n");
+		fprintf(fp_help, "  Input/output:\n");
+		fprintf(fp_help, "    -t INT       number of threads [%d]\n", n_threads);
+		fprintf(fp_help, "    -o FILE      output mappings to FILE [stdout]\n");
+		fprintf(fp_help, "    -K NUM       minibatch size for mapping [500M]\n");
+		fprintf(fp_help, "    -S           output linear chains in * sName sLen nMz div sStart sEnd qStart qEnd\n");
+		fprintf(fp_help, "    --vc         output in the vertex coordinate\n");
+		fprintf(fp_help, "  Preset:\n");
+		fprintf(fp_help, "    -x STR       preset []\n");
+		fprintf(fp_help, "                 - lr: noisy long read mapping (the default)\n");
+		fprintf(fp_help, "                 - asm: asm-to-ref mapping\n");
+		fprintf(fp_help, "                 - sr: short reads\n");
+		fprintf(fp_help, "                 - ggs: incremental graph generation\n");
+		return fp_help == stdout? 0 : 1;
+	}
+
+	g = gfa_read(argv[o.ind]);
+	if (g == 0) {
+		fprintf(stderr, "[ERROR] failed to load the graph from file '%s'\n", argv[o.ind]);
+		return 1;
+	} else if (mg_verbose >= 3) {
+		fprintf(stderr, "[M::%s::%.3f*%.2f] loaded the graph from \"%s\"\n", __func__, realtime() - mg_realtime0, cputime() / (realtime() - mg_realtime0), argv[o.ind]);
+	}
+
+	if (gpt.algo == MG_G_NONE && !(gpt.flag & MG_G_CALL)) {
+		ret = mg_map_files(g, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &ipt, &opt, n_threads);
+	} else {
+		if (gpt.flag & MG_G_CALL) gfa_sort_ref_arc(g);
+		ret = mg_ggen(g, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &ipt, &opt, &gpt, n_threads);
+	}
+
+	if ((gpt.algo != MG_G_NONE || (opt.flag & MG_M_CAL_COV)) && !(gpt.flag & MG_G_CALL))
+		gfa_print(g, stdout, 0);
+	gfa_destroy(g);
+
+	if (fflush(stdout) == EOF) {
+		fprintf(stderr, "[ERROR] failed to write the results\n");
+		exit(EXIT_FAILURE);
+	}
+
+	if (mg_verbose >= 3) {
+		fprintf(stderr, "[M::%s] Version: %s\n", __func__, MG_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() - mg_realtime0, cputime(), peakrss() / 1024.0 / 1024.0 / 1024.0);
+	}
+	return !!ret;
+}