r156: removed fastsim

dfs.c

@@ -275,69 +275,3 @@ int main_count(int argc, char *argv[])
 	free(d.str);
 	return 0;
 }
-
-/***********
- * fastsim *
- ***********/
-
-#include "fermi2.h"
-#include "khash.h"
-KHASH_MAP_INIT_INT64(64, int)
-
-typedef struct {
-	const rld_t *e;
-	const fmsa_t *sa;
-	int k, max_occ;
-	kstring_t *s;
-} dfs_sim_t;
-
-static void dfs_sim2(void *data, int tid, int k, char *path, const rldintv_t *ik, const rldintv_t *ok, int *cont)
-{
-	dfs_sim_t *d = (dfs_sim_t*)data;
-	int c, i;
-	kstring_t *s;
-	for (c = 0; c < 6; ++c)
-		if (ok[c].x[2] < 2) *cont &= ~(1<<c);
-	if (k < d->k || ik->x[2] > d->max_occ || ik->x[2] < 2) return;
-	s = &d->s[tid];
-	s->l = 0;
-	for (i = 0; i < ik->x[2]; ++i) {
-		int64_t si;
-		fm_sa(d->e, d->sa, ik->x[0] + i, &si);
-		if (i) kputc('\t', s);
-		kputl(si, s);
-	}
-	puts(s->s);
-}
-
-int main_fastsim(int argc, char *argv[])
-{
-	int i, c, n_threads = 1;
-	rld_t *e;
-	fmsa_t *sa;
-	dfs_sim_t d;
-
-	d.k = 23, d.max_occ = 500;
-	while ((c = getopt(argc, argv, "t:k:m:")) >= 0) {
-		if (c == 't') n_threads = atoi(optarg);
-		else if (c == 'k') d.k = atoi(optarg);
-		else if (c == 'm') d.max_occ = atoi(optarg);
-	}
-	if (optind + 2 > argc) {
-		fprintf(stderr, "Usage: fermi2 fastsim [-t nThreads=%d] [-k kmer=%d] [-m maxOcc=%d] <in.fmd> <in.sa>\n", n_threads, d.k, d.max_occ);
-		return 1;
-	}
-	// initialize
-	e = rld_restore(argv[optind]);
-	sa = fm_sa_restore(argv[optind+1]);
-	d.e = e; d.sa = sa;
-	d.s = calloc(n_threads, sizeof(kstring_t));
-	// collect counts
-	fm_dfs(1, &e, 1, d.k, n_threads, 0, dfs_sim2, &d);
-	// free
-	fm_sa_destroy(sa);
-	rld_destroy(e);
-	for (i = 0; i < n_threads; ++i) free(d.s[i].s);
-	free(d.s);
-	return 0;
-}

fermi2.h

@@ -4,7 +4,7 @@
 #include <stdint.h>
 #include "rld0.h"
 
-#define FM_VERSION "r155"
+#define FM_VERSION "r156"
 
 #define fmd_comp(a) ((a) >= 1 && (a) <= 4? 5 - (a) : (a))
 #define fmd_set_intv(e, c, ik) ((ik).x[0] = (e)->cnt[(int)(c)], (ik).x[2] = (e)->cnt[(int)(c)+1] - (e)->cnt[(int)(c)], (ik).x[1] = (e)->cnt[fmd_comp(c)], (ik).info = 0)

main.c

@@ -15,7 +15,6 @@ int main_assemble(int argc, char *argv[]);
 int main_simplify(int argc, char *argv[]);
 int main_sa(int argc, char *argv[]);
 int main_match(int argc, char *argv[]);
-int main_fastsim(int argc, char *argv[]);
 
 void liftrlimit(void);
 double cputime(void);
@@ -59,7 +58,6 @@ int main(int argc, char *argv[])
 	else if (strcmp(argv[1], "simplify") == 0) ret = main_simplify(argc-1, argv+1);
 	else if (strcmp(argv[1], "sa") == 0) ret = main_sa(argc-1, argv+1);
 	else if (strcmp(argv[1], "match") == 0) ret = main_match(argc-1, argv+1);
-	else if (strcmp(argv[1], "fastsim") == 0) ret = main_fastsim(argc-1, argv+1);
 	else {
 		fprintf(stderr, "[E::%s] unknown command\n", __func__);
 		return 1;