ruby-minigraph 0.0.20.0

data/ext/minigraph/gfa-io.c

@@ -0,0 +1,395 @@
+#include <zlib.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include "kstring.h"
+#include "gfa-priv.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 65536)
+
+/***********
+ * Tag I/O *
+ ***********/
+
+int gfa_aux_parse(char *s, uint8_t **data, int *max)
+{
+	char *q, *p;
+	kstring_t str;
+	if (s == 0) return 0;
+	str.l = 0, str.m = *max, str.s = (char*)*data;
+	if (*s == '\t') ++s;
+	for (p = q = s;; ++p) {
+		if (*p == 0 || *p == '\t') {
+			int c = *p;
+			*p = 0;
+			if (p - q >= 5 && q[2] == ':' && q[4] == ':' && (q[3] == 'A' || q[3] == 'i' || q[3] == 'f' || q[3] == 'Z' || q[3] == 'B')) {
+				int type = q[3];
+				kputsn_(q, 2, &str);
+				q += 5;
+				if (type == 'A') {
+					kputc_('A', &str);
+					kputc_(*q, &str);
+				} else if (type == 'i') {
+					int32_t x;
+					x = strtol(q, &q, 10);
+					kputc_(type, &str); kputsn_((char*)&x, 4, &str);
+				} else if (type == 'f') {
+					float x;
+					x = strtod(q, &q);
+					kputc_('f', &str); kputsn_(&x, 4, &str);
+				} else if (type == 'Z') {
+					kputc_('Z', &str); kputsn_(q, p - q + 1, &str); // note that this include the trailing NULL
+				} else if (type == 'B') {
+					type = *q++; // q points to the first ',' following the typing byte
+					if (p - q >= 2 && (type == 'c' || type == 'C' || type == 's' || type == 'S' || type == 'i' || type == 'I' || type != 'f')) {
+						int32_t n;
+						char *r;
+						for (r = q, n = 0; *r; ++r)
+							if (*r == ',') ++n;
+						kputc_('B', &str); kputc_(type, &str); kputsn_(&n, 4, &str);
+						// TODO: to evaluate which is faster: a) aligned array and then memmove(); b) unaligned array; c) kputsn_()
+						if (type == 'c')      while (q + 1 < p) { int8_t   x = strtol(q + 1, &q, 0); kputc_(x, &str); }
+						else if (type == 'C') while (q + 1 < p) { uint8_t  x = strtol(q + 1, &q, 0); kputc_(x, &str); }
+						else if (type == 's') while (q + 1 < p) { int16_t  x = strtol(q + 1, &q, 0); kputsn_(&x, 2, &str); }
+						else if (type == 'S') while (q + 1 < p) { uint16_t x = strtol(q + 1, &q, 0); kputsn_(&x, 2, &str); }
+						else if (type == 'i') while (q + 1 < p) { int32_t  x = strtol(q + 1, &q, 0); kputsn_(&x, 4, &str); }
+						else if (type == 'I') while (q + 1 < p) { uint32_t x = strtol(q + 1, &q, 0); kputsn_(&x, 4, &str); }
+						else if (type == 'f') while (q + 1 < p) { float    x = strtod(q + 1, &q);    kputsn_(&x, 4, &str); }
+					}
+				} // should not be here, as we have tested all types
+			}
+			q = p + 1;
+			if (c == 0) break;
+		}
+	}
+	if (str.l > 0 && str.l == str.m) ks_resize(&str, str.l + 1);
+	if (str.s) str.s[str.l] = 0;
+	*max = str.m, *data = (uint8_t*)str.s;
+	return str.l;
+}
+
+int gfa_aux_format(int l_aux, const uint8_t *aux, char **t, int *max)
+{
+	kstring_t str;
+	const uint8_t *s = aux;
+	str.l = 0, str.s = *t, str.m = *max;
+	while (s < aux + l_aux) {
+		uint8_t type, key[2];
+		key[0] = s[0]; key[1] = s[1];
+		s += 2; type = *s++;
+		kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str);
+		if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; }
+		else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; }
+		else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
+		else if (type == 'Z') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
+		else if (type == 'B') {
+			uint8_t sub_type = *(s++);
+			int32_t i, n;
+			memcpy(&n, s, 4);
+			s += 4; // no point to the start of the array
+			kputsn("B:", 2, &str); kputc(sub_type, &str); // write the typing
+			for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if"
+				kputc(',', &str);
+				if ('c' == sub_type)      { kputw(*(int8_t*)s, &str); ++s; }
+				else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
+				else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
+				else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
+				else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
+				else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
+				else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
+			}
+		}
+	}
+	*t = str.s, *max = str.m;
+	return str.l;
+}
+
+/****************
+ * Line parsers *
+ ****************/
+
+int gfa_parse_S(gfa_t *g, char *s)
+{
+	int i, is_ok = 0;
+	char *p, *q, *seg = 0, *seq = 0, *rest = 0;
+	uint32_t sid, len = 0;
+	for (i = 0, p = q = s + 2;; ++p) {
+		if (*p == 0 || *p == '\t') {
+			int c = *p;
+			*p = 0;
+			if (i == 0) seg = q;
+			else if (i == 1) {
+				seq = q[0] == '*'? 0 : gfa_strdup(q);
+				is_ok = 1, rest = c? p + 1 : 0;
+				break;
+			}
+			++i, q = p + 1;
+			if (c == 0) break;
+		}
+	}
+	if (is_ok) { // all mandatory fields read
+		int l_aux, m_aux = 0, LN = -1;
+		uint8_t *aux = 0, *s_LN = 0;
+		gfa_seg_t *s;
+		l_aux = gfa_aux_parse(rest, &aux, &m_aux); // parse optional tags
+		s_LN = l_aux? gfa_aux_get(l_aux, aux, "LN") : 0;
+		if (s_LN && s_LN[0] == 'i') {
+			LN = *(int32_t*)(s_LN + 1);
+			l_aux = gfa_aux_del(l_aux, aux, s_LN);
+		}
+		if (seq == 0) {
+			if (LN >= 0) len = LN;
+		} else len = strlen(seq);
+		if (LN >= 0 && len != LN && gfa_verbose >= 2)
+			fprintf(stderr, "[W] for segment '%s', LN:i:%d tag is different from sequence length %d\n", seg, LN, len);
+		sid = gfa_add_seg(g, seg);
+		s = &g->seg[sid];
+		s->len = len, s->seq = seq;
+		if (l_aux > 0) {
+			uint8_t *s_SN = 0, *s_SO = 0, *s_SR = 0;
+			s_SN = gfa_aux_get(l_aux, aux, "SN");
+			if (s_SN && *s_SN == 'Z') { // then parse stable tags
+				s->snid = gfa_sseq_add(g, (char*)(s_SN + 1)), s->soff = 0;
+				l_aux = gfa_aux_del(l_aux, aux, s_SN);
+				s_SO = gfa_aux_get(l_aux, aux, "SO");
+				if (s_SO && *s_SO == 'i') {
+					s->soff = *(int32_t*)(s_SO + 1);
+					l_aux = gfa_aux_del(l_aux, aux, s_SO);
+				}
+			}
+			s_SR = gfa_aux_get(l_aux, aux, "SR");
+			if (s_SR && *s_SR == 'i') {
+				s->rank = *(int32_t*)(s_SR + 1);
+				if (s->rank > g->max_rank) g->max_rank = s->rank;
+				l_aux = gfa_aux_del(l_aux, aux, s_SR);
+			}
+			gfa_sseq_update(g, s);
+		}
+		if (l_aux > 0)
+			s->aux.m_aux = m_aux, s->aux.l_aux = l_aux, s->aux.aux = aux;
+		else if (aux)
+			free(aux);
+	} else return -1;
+	return 0;
+}
+
+int gfa_parse_L(gfa_t *g, char *s)
+{
+	int i, oriv = -1, oriw = -1, is_ok = 0;
+	char *p, *q, *segv = 0, *segw = 0, *rest = 0;
+	int32_t ov = INT32_MAX, ow = INT32_MAX;
+	for (i = 0, p = q = s + 2;; ++p) {
+		if (*p == 0 || *p == '\t') {
+			int c = *p;
+			*p = 0;
+			if (i == 0) {
+				segv = q;
+			} else if (i == 1) {
+				if (*q != '+' && *q != '-') return -2;
+				oriv = (*q != '+');
+			} else if (i == 2) {
+				segw = q;
+			} else if (i == 3) {
+				if (*q != '+' && *q != '-') return -2;
+				oriw = (*q != '+');
+			} else if (i == 4) {
+				if (*q == '*') {
+					ov = ow = 0;
+				} else if (*q == ':') {
+					ov = INT32_MAX;
+					ow = isdigit(*(q+1))? strtol(q+1, &q, 10) : INT32_MAX;
+				} else if (isdigit(*q)) {
+					char *r;
+					ov = strtol(q, &r, 10);
+					if (isupper(*r)) { // CIGAR
+						ov = ow = 0;
+						do {
+							long l;
+							l = strtol(q, &q, 10);
+							if (*q == 'M' || *q == 'D' || *q == 'N') ov += l;
+							if (*q == 'M' || *q == 'I' || *q == 'S') ow += l;
+							++q;
+						} while (isdigit(*q));
+					} else if (*r == ':') { // overlap lengths
+						ow = isdigit(*(r+1))? strtol(r+1, &r, 10) : INT32_MAX;
+					} else break;
+				} else break;
+				is_ok = 1, rest = c? p + 1 : 0;
+				break;
+			}
+			++i, q = p + 1;
+			if (c == 0) break;
+		}
+	}
+	if (i == 4 && is_ok == 0) ov = ow = 0, is_ok = 1; // no overlap field
+	if (is_ok) {
+		uint32_t v, w;
+		int l_aux, m_aux = 0;
+		uint8_t *aux = 0;
+		gfa_arc_t *arc;
+		v = gfa_add_seg(g, segv) << 1 | oriv;
+		w = gfa_add_seg(g, segw) << 1 | oriw;
+		arc = gfa_add_arc1(g, v, w, ov, ow, -1, 0);
+		l_aux = gfa_aux_parse(rest, &aux, &m_aux); // parse optional tags
+		if (l_aux) {
+			gfa_aux_t *a = &g->link_aux[arc->link_id];
+			uint8_t *s_L1, *s_L2, *s_SR;
+			a->l_aux = l_aux, a->m_aux = m_aux, a->aux = aux;
+			s_SR = gfa_aux_get(a->l_aux, a->aux, "SR");
+			if (s_SR && s_SR[0] == 'i') {
+				arc->rank = *(int32_t*)(s_SR+1);
+				a->l_aux = gfa_aux_del(a->l_aux, a->aux, s_SR);
+			}
+			s_L1 = gfa_aux_get(a->l_aux, a->aux, "L1");
+			if (s_L1) {
+				if (ov != INT32_MAX && s_L1[0] == 'i')
+					g->seg[v>>1].len = g->seg[v>>1].len > ov + *(int32_t*)(s_L1+1)? g->seg[v>>1].len : ov + *(int32_t*)(s_L1+1);
+				a->l_aux = gfa_aux_del(a->l_aux, a->aux, s_L1);
+			}
+			s_L2 = gfa_aux_get(a->l_aux, a->aux, "L2");
+			if (s_L2) {
+				if (ow != INT32_MAX && s_L2[0] == 'i')
+					g->seg[w>>1].len = g->seg[w>>1].len > ow + *(int32_t*)(s_L2+1)? g->seg[w>>1].len : ow + *(int32_t*)(s_L2+1);
+				a->l_aux = gfa_aux_del(a->l_aux, a->aux, s_L2);
+			}
+			if (a->l_aux == 0) {
+				free(a->aux);
+				a->aux = 0, a->m_aux = 0;
+			}
+		}
+	} else return -1;
+	return 0;
+}
+
+static gfa_seg_t *gfa_parse_fa_hdr(gfa_t *g, char *s)
+{
+	int32_t i;
+	char buf[16];
+	gfa_seg_t *seg;
+	for (i = 0; s[i]; ++i)
+		if (isspace(s[i])) break;
+	s[i] = 0;
+	sprintf(buf, "s%d", g->n_seg + 1);
+	i = gfa_add_seg(g, buf);
+	seg = &g->seg[i];
+	seg->snid = gfa_sseq_add(g, s + 1);
+	seg->soff = seg->rank = 0;
+	return seg;
+}
+
+static void gfa_update_fa_seq(gfa_t *g, gfa_seg_t *seg, int32_t l_seq, const char *seq)
+{
+	if (seg == 0) return;
+	seg->seq = gfa_strdup(seq);
+	seg->len = l_seq;
+	gfa_sseq_update(g, seg);
+}
+
+/****************
+ * User-end I/O *
+ ****************/
+
+gfa_t *gfa_read(const char *fn)
+{
+	gzFile fp;
+	gfa_t *g;
+	kstring_t s = {0,0,0}, fa_seq = {0,0,0};
+	kstream_t *ks;
+	int dret, is_fa = 0;
+	gfa_seg_t *fa_seg = 0;
+	uint64_t lineno = 0;
+
+	fp = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(0, "r");
+	if (fp == 0) return 0;
+	ks = ks_init(fp);
+	g = gfa_init();
+	while (ks_getuntil(ks, KS_SEP_LINE, &s, &dret) >= 0) {
+		int ret = 0;
+		++lineno;
+		if (s.l > 0 && s.s[0] == '>') { // FASTA header
+			is_fa = 1;
+			if (fa_seg) gfa_update_fa_seq(g, fa_seg, fa_seq.l, fa_seq.s);
+			fa_seg = gfa_parse_fa_hdr(g, s.s);
+			fa_seq.l = 0;
+		} else if (is_fa) { // FASTA mode
+			if (s.l >= 3 && s.s[1] == '\t') { // likely a GFA line
+				gfa_update_fa_seq(g, fa_seg, fa_seq.l, fa_seq.s); // finalize fa_seg
+				fa_seg = 0;
+				is_fa = 0;
+			} else kputsn(s.s, s.l, &fa_seq); // likely a FASTA sequence line
+		}
+		if (is_fa) continue;
+		if (s.l < 3 || s.s[1] != '\t') continue; // empty line
+		if (s.s[0] == 'S') ret = gfa_parse_S(g, s.s);
+		else if (s.s[0] == 'L') ret = gfa_parse_L(g, s.s);
+		if (ret < 0 && gfa_verbose >= 1)
+			fprintf(stderr, "[E] invalid %c-line at line %ld (error code %d)\n", s.s[0], (long)lineno, ret);
+	}
+	if (is_fa && fa_seg) gfa_update_fa_seq(g, fa_seg, fa_seq.l, fa_seq.s);
+	free(fa_seq.s);
+	free(s.s);
+	gfa_finalize(g);
+	ks_destroy(ks);
+	gzclose(fp);
+	return g;
+}
+
+void gfa_print(const gfa_t *g, FILE *fp, int flag)
+{
+	uint32_t i;
+	uint64_t k;
+	for (i = 0; i < g->n_seg; ++i) {
+		const gfa_seg_t *s = &g->seg[i];
+		if (s->del) continue;
+		fprintf(fp, "S\t%s\t", s->name);
+		if (s->seq && !(flag & GFA_O_NO_SEQ)) fputs(s->seq, fp);
+		else fputc('*', fp);
+		fprintf(fp, "\tLN:i:%d", s->len);
+		if (s->snid >= 0 && s->soff >= 0)
+			fprintf(fp, "\tSN:Z:%s\tSO:i:%d", g->sseq[s->snid].name, s->soff);
+		if (s->rank >= 0)
+			fprintf(fp, "\tSR:i:%d", s->rank);
+		if (s->utg && s->utg->n) fprintf(fp, "\tRC:i:%d\tlc:i:%d", s->utg->n, s->utg->len_comp);
+		if (s->aux.l_aux > 0) {
+			char *t = 0;
+			int max = 0;
+			gfa_aux_format(s->aux.l_aux, s->aux.aux, &t, &max);
+			fputs(t, fp);
+			free(t);
+		}
+		fputc('\n', fp);
+		if (s->utg && s->utg->n) {
+			uint32_t j, l;
+			for (j = l = 0; j < s->utg->n; ++j) {
+				const gfa_utg_t *u = s->utg;
+				fprintf(fp, "A\t%s\t%d\t%c\t%s\t%d\t%d\n", s->name, l, "+-"[u->a[j]>>32&1], u->name[j], (int32_t)(u->r[j]>>32), (int32_t)u->r[j]);
+				l += (uint32_t)u->a[j];
+			}
+		}
+	}
+	for (k = 0; k < g->n_arc; ++k) {
+		const gfa_arc_t *a = &g->arc[k];
+		const gfa_aux_t *aux = a->link_id < g->n_arc? &g->link_aux[a->link_id] : 0;
+		if (a->del || a->comp) continue;
+		fprintf(fp, "L\t%s\t%c\t%s\t%c", g->seg[a->v_lv>>33].name, "+-"[a->v_lv>>32&1], g->seg[a->w>>1].name, "+-"[a->w&1]);
+		if (!(flag & GFA_O_OV_EXT)) {
+			fprintf(fp, "\t%dM", a->ov < a->ow? a->ov : a->ow);
+		} else {
+			if (a->ov == a->ow) fprintf(fp, "\t%dM", a->ov);
+			else fprintf(fp, "\t%d:%d", a->ov, a->ow);
+		}
+		if (a->rank >= 0) fprintf(fp, "\tSR:i:%d", a->rank);
+		fprintf(fp, "\tL1:i:%d", gfa_arc_len(*a));
+		fprintf(fp, "\tL2:i:%d", gfa_arc_lw(g, *a));
+		if (aux && aux->l_aux) {
+			char *t = 0;
+			int max = 0;
+			gfa_aux_format(aux->l_aux, aux->aux, &t, &max);
+			if (t) fputs(t, fp);
+			free(t);
+		}
+		fputc('\n', fp);
+	}
+}

data/ext/minigraph/gfa-priv.h

@@ -0,0 +1,154 @@
+#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))))
+#define GFA_CALLOC(ptr, len) ((ptr) = (__typeof__(ptr))calloc((len), sizeof(*(ptr))))
+#define GFA_REALLOC(ptr, len) ((ptr) = (__typeof__(ptr))realloc((ptr), (len) * sizeof(*(ptr))))
+#define GFA_BZERO(ptr, len) memset((ptr), 0, (len) * sizeof(*(ptr)))
+#define GFA_EXPAND(a, m) do { \
+		(m) = (m)? (m) + ((m)>>1) : 16; \
+		GFA_REALLOC((a), (m)); \
+	} while (0)
+
+typedef struct { uint64_t x, y; } gfa128_t;
+
+// linearized subgraphs
+
+typedef struct {
+	uint32_t v, d;
+	int32_t off, n;
+} gfa_subv_t;
+
+typedef struct {
+	int32_t n_v, n_a, is_dag;
+	gfa_subv_t *v;
+	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 is_bidir, n_seg, len_max, len_min;
+	uint32_t *v, n_paths;
+	char *seq_max, *seq_min; // seq_max and seq_min point to v[]
+} gfa_bubble_t;
+
+struct gfa_scbuf_s;
+typedef struct gfa_scbuf_s gfa_scbuf_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+char *gfa_strdup(const char *src);
+char *gfa_strndup(const char *src, size_t n);
+void radix_sort_gfa64(uint64_t *st, uint64_t *en);
+
+// add/delete one segment/arc/stable sequence
+int32_t gfa_add_seg(gfa_t *g, const char *name);
+gfa_arc_t *gfa_add_arc1(gfa_t *g, uint32_t v, uint32_t w, int32_t ov, int32_t ow, int64_t link_id, int comp);
+int32_t gfa_sseq_get(const gfa_t *g, const char *sname);
+int32_t gfa_sseq_add(gfa_t *g, const char *sname);
+void gfa_sseq_update(gfa_t *g, const gfa_seg_t *s);
+
+// whole graph operations
+void gfa_arc_sort(gfa_t *g);
+void gfa_arc_index(gfa_t *g);
+uint32_t gfa_fix_symm_add(gfa_t *g);
+void gfa_fix_symm_del(gfa_t *g); // delete multiple edges and restore skew-symmetry
+void gfa_arc_rm(gfa_t *g);
+void gfa_cleanup(gfa_t *g); // permanently delete arcs marked as deleted, sort and then index
+void gfa_finalize(gfa_t *g);
+int32_t gfa_check_multi(const gfa_t *g);
+uint32_t gfa_fix_multi(gfa_t *g);
+
+int gfa_arc_del_multi_risky(gfa_t *g);
+int gfa_arc_del_asymm_risky(gfa_t *g);
+
+// edit distance
+typedef struct {
+	int32_t traceback;
+	int32_t bw_dyn, max_lag, max_chk;
+	int32_t s_term;
+	int64_t i_term;
+} gfa_edopt_t;
+
+typedef struct {
+	int32_t s;
+	uint32_t end_v;
+	int32_t end_off;
+	int32_t wlen; // length of walk
+	int32_t n_end;
+	int32_t nv;
+	int64_t n_iter;
+	int32_t *v;
+} gfa_edrst_t;
+
+void gfa_edopt_init(gfa_edopt_t *opt);
+void *gfa_ed_init(void *km, const gfa_edopt_t *opt, const gfa_t *g, const gfa_edseq_t *es, int32_t ql, const char *q, uint32_t v0, int32_t off0);
+void gfa_ed_step(void *z_, uint32_t v1, int32_t off1, int32_t s_term, gfa_edrst_t *r);
+void gfa_ed_destroy(void *z_);
+
+int32_t gfa_edit_dist(void *km, const gfa_edopt_t *opt, const gfa_t *g, const gfa_edseq_t *es, int32_t ql, const char *q, uint32_t v0, int32_t off0, gfa_edrst_t *rst);
+
+// assembly related routines
+int gfa_arc_del_trans(gfa_t *g, int fuzz); // transitive reduction
+int gfa_arc_del_weak(gfa_t *g);
+int gfa_arc_pair_strong(gfa_t *g);
+int gfa_arc_del_short(gfa_t *g, int min_ovlp_len, float drop_ratio); // delete short arcs
+int gfa_drop_tip(gfa_t *g, int tip_cnt, int tip_len); // cut tips
+int gfa_drop_internal(gfa_t *g, int max_ext);
+int gfa_cut_z(gfa_t *g, int32_t min_dist, int32_t max_dist);
+int gfa_topocut(gfa_t *g, float drop_ratio, int32_t tip_cnt, int32_t tip_len);
+int gfa_bub_simple(gfa_t *g, int min_side, int max_side);
+int gfa_pop_bubble(gfa_t *g, int radius, int max_del, int protect_tip); // bubble popping
+gfa_t *gfa_ug_gen(const gfa_t *g);
+void gfa_scc_all(const gfa_t *g);
+
+// subset, modifying the graph
+void gfa_sub(gfa_t *g, int n, char *const* seg, int step);
+char **gfa_query_by_reg(const gfa_t *g, int32_t n_bb, const gfa_bubble_t *bb, const char *reg, int *n_seg);
+
+// subset, without modifying the graph
+gfa_sub_t *gfa_sub_from(void *km0, const gfa_t *g, uint32_t v0, int32_t max_dist);
+void gfa_sub_destroy(gfa_sub_t *sub);
+void gfa_sub_print(FILE *fp, const gfa_t *g, const gfa_sub_t *sub);
+
+gfa_scbuf_t *gfa_scbuf_init(const gfa_t *g);
+gfa_sub_t *gfa_scc1(void *km0, const gfa_t *g, gfa_scbuf_t *b, uint32_t v0);
+void gfa_scbuf_destroy(gfa_scbuf_t *b);
+
+// graph augmentation
+int gfa_ins_adj(const gfa_t *g, int min_len, gfa_ins_t *ins, const char *seq);
+int32_t gfa_ins_filter(const gfa_t *g, int32_t n_ins, gfa_ins_t *ins);
+void gfa_augment(gfa_t *g, int32_t n_ins, const gfa_ins_t *ins, int32_t n_ctg, const char *const* name, const char *const* seq);
+
+gfa_sfa_t *gfa_gfa2sfa(const gfa_t *g, int32_t *n_sfa_, int32_t write_seq);
+
+void gfa_sort_ref_arc(gfa_t *g);
+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);
+
+void gfa_sql_write(FILE *fp, const gfa_t *g, int write_seq);
+
+static inline int64_t gfa_find_arc(const gfa_t *g, uint32_t v, uint32_t w)
+{
+	uint32_t i, nv = gfa_arc_n(g, v), nw = 0, k = (uint32_t)-1;
+	gfa_arc_t *av = gfa_arc_a(g, v);
+	for (i = 0; i < nv; ++i)
+		if (av[i].w == w) ++nw, k = i;
+	return nw == 1? (int64_t)(&av[k] - g->arc) : nw == 0? -1 : -2;
+}
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif // ~__GFA_PRIV_H__