r307: sync with lh3/gfatools@5f7fe55

gfa-base.c

@@ -210,10 +210,16 @@ void gfa_fix_arc_len(gfa_t *g)
 	for (k = 0; k < g->n_arc; ++k) {
 		gfa_arc_t *a = &g->arc[k];
 		uint32_t v = gfa_arc_head(*a), w = gfa_arc_tail(*a);
-		if (g->seg[v>>1].del || g->seg[w>>1].del) {
+		const gfa_seg_t *sv = &g->seg[v>>1];
+		if (!sv->del && sv->len < a->ov) {
+			if (gfa_verbose >= 2)
+				fprintf(stderr, "[W] overlap length longer than segment length for '%s': %d > %d\n", sv->name, a->ov, sv->len);
+			a->ov = sv->len;
+		}
+		if (sv->del || g->seg[w>>1].del) {
 			a->del = 1;
 		} else {
-			a->v_lv |= g->seg[v>>1].len - a->ov;
+			a->v_lv |= sv->len - a->ov;
 		}
 	}
 }
@@ -296,6 +302,11 @@ void gfa_arc_rm(gfa_t *g)
 		uint32_t u = g->arc[e].v_lv>>32, v = g->arc[e].w;
 		if (!g->arc[e].del && !g->seg[u>>1].del && !g->seg[v>>1].del)
 			g->arc[n++] = g->arc[e];
+		else {
+			gfa_aux_t *aux = &g->link_aux[g->arc[e].link_id];
+			free(aux->aux);
+			aux->aux = 0, aux->l_aux = aux->m_aux = 0;
+		}
 	}
 	if (n < g->n_arc) { // arc index is out of sync
 		if (g->idx) free(g->idx);
@@ -325,7 +336,7 @@ int32_t gfa_check_multi(const gfa_t *g)
 		int32_t nv = gfa_arc_n(g, v);
 		max_nv = max_nv > nv? max_nv : nv;
 	}
-	if (max_nv == 1) return 0;
+	if (max_nv == 1 || max_nv < 0) return 0;
 	GFA_MALLOC(buf, max_nv);
 	for (v = 0; v < n_vtx; ++v) {
 		int32_t i, s, nv = gfa_arc_n(g, v);
@@ -422,7 +433,7 @@ static inline int gfa_aux_type2size(int x)
 }
 
 #define __skip_tag(s) do { \
-		int type = toupper(*(s)); \
+		int type = *(s); \
 		++(s); \
 		if (type == 'Z') { while (*(s)) ++(s); ++(s); } \
 		else if (type == 'B') (s) += 5 + gfa_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \

gfa-priv.h

@@ -1,6 +1,7 @@
 #ifndef __GFA_PRIV_H__
 #define __GFA_PRIV_H__
 
+#include <stdlib.h>
 #include "gfa.h"
 
 #define GFA_MALLOC(ptr, len) ((ptr) = (__typeof__(ptr))malloc((len) * sizeof(*(ptr))))
@@ -24,10 +25,19 @@ typedef struct {
 typedef struct {
 	int32_t n_v, n_a, is_dag;
 	gfa_subv_t *v;
-	int32_t *a;
+	uint64_t *a; // high 32 bits: point to the neighbor; low 32 bit: arc index in the graph
 	void *km;
 } gfa_sub_t;
 
+typedef struct {
+	int32_t snid, ss, se;
+	uint32_t vs, ve;
+	int32_t n_seg, len_max, len_min;
+	float cf_max, cf_min;
+	uint32_t *v;
+	char *seq_max, *seq_min; // seq_max and seq_min point to v[]
+} gfa_bubble_t;
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -58,9 +68,11 @@ uint32_t gfa_fix_multi(gfa_t *g);
 int gfa_arc_del_trans(gfa_t *g, int fuzz); // transitive reduction
 int gfa_arc_del_short(gfa_t *g, float drop_ratio); // delete short arcs
 int gfa_cut_tip(gfa_t *g, int max_ext); // cut tips
+int gfa_topocut(gfa_t *g, int max_ext, float drop_ratio);
+int gfa_bub_simple(gfa_t *g, int min_side, int max_side);
 int gfa_cut_internal(gfa_t *g, int max_ext); // drop internal segments
 int gfa_cut_biloop(gfa_t *g, int max_ext); // Hmm... I forgot... Some type of weird local topology
-int gfa_pop_bubble(gfa_t *g, int max_dist); // bubble popping
+int gfa_pop_bubble(gfa_t *g, int max_dist, int protect_tip); // bubble popping
 gfa_t *gfa_ug_gen(const gfa_t *g);
 
 // subset, modifying the graph
@@ -78,7 +90,9 @@ void gfa_augment(gfa_t *g, int32_t n_ins, const gfa_ins_t *ins, int32_t n_ctg, c
 
 gfa_sfa_t *gfa_gfa2sfa(const gfa_t *g, int32_t *n_sfa_, int32_t write_seq);
 
-void gfa_blacklist_print(const gfa_t *g, FILE *fp, int32_t min_len); // FIXME: doesn't work with translocations
+gfa_bubble_t *gfa_bubble(const gfa_t *g, int32_t *n_); // FIXME: doesn't work with translocation
+
+void gfa_gt_simple_print(const gfa_t *g, float min_dc, int32_t is_path); // FIXME: doesn't work with translocations
 
 void gfa_aux_update_cv(gfa_t *g, const char *tag, const double *cov_seg, const double *cov_link);
 

gfa.h

@@ -4,7 +4,7 @@
 #include <stdio.h>
 #include <stdint.h>
 
-#define GFA_VERSION "0.3-r70"
+#define GFA_VERSION "0.3-r116-dirty"
 
 #define GFA_O_OV_EXT   0x1
 #define GFA_O_NO_SEQ   0x2

minigraph.h

@@ -4,7 +4,7 @@
 #include <stdint.h>
 #include "gfa.h"
 
-#define MG_VERSION "0.6-r306-dirty"
+#define MG_VERSION "0.6-r307-dirty"
 
 #define MG_M_SPLICE       0x10
 #define MG_M_SR           0x20