ruby-minigraph 0.0.20.0

data/ext/minigraph/gfa-bbl.c

@@ -0,0 +1,372 @@
+#include <assert.h>
+#include <stdio.h>
+#include "gfa-priv.h"
+#include "kalloc.h"
+#include "ksort.h"
+#include "kvec.h"
+
+#define generic_key(x) (x)
+KRADIX_SORT_INIT(gfa32, uint32_t, generic_key, 4)
+
+void gfa_sort_ref_arc(gfa_t *g)
+{
+	uint32_t v, n_vtx = gfa_n_vtx(g);
+	for (v = 0; v < n_vtx; ++v) {
+		gfa_seg_t *s = &g->seg[v>>1];
+		int32_t i, nv;
+		gfa_arc_t *av, b;
+		if (s->rank != 0) continue;
+		nv = gfa_arc_n(g, v);
+		av = gfa_arc_a(g, v);
+		for (i = 0; i < nv; ++i) {
+			uint32_t w = av[i].w;
+			gfa_seg_t *t = &g->seg[w>>1];
+			if (t->rank == 0 && t->snid == s->snid && (v&1) == (w&1)) {
+				if (((v&1) == 0 && s->soff + s->len == t->soff) || ((v&1) == 1 && t->soff + t->len == s->soff))
+					break;
+			}
+		}
+		if (nv > 0 && i == nv) fprintf(stderr, "X\t%c%s\t%d\t%s\t%d\n", "><"[v&1], s->name, i, g->sseq[s->snid].name, s->soff);
+		assert(nv == 0 || i < nv);
+		if (i > 0 && i < nv) b = av[i], av[i] = av[0], av[0] = b;
+	}
+}
+
+void gfa_sub_print(FILE *fp, const gfa_t *g, const gfa_sub_t *sub)
+{
+	int32_t i, j;
+	for (i = 0; i < sub->n_v; ++i) {
+		gfa_subv_t *p = &sub->v[i];
+		fprintf(fp, "[%d]\t%d\t%c%s\t%d\t%d", i, p->v, "><"[p->v&1], g->seg[p->v>>1].name, p->d, p->n);
+		if (p->n > 0) {
+			fputc('\t', fp);
+			for (j = 0; j < p->n; ++j) {
+				if (j) fputc(',', fp);
+				fprintf(fp, "%d", (uint32_t)(sub->a[p->off + j]>>32));
+			}
+		}
+		fputc('\n', fp);
+	}
+}
+
+/****************
+ * Tarjan's SCC *
+ ****************/
+
+typedef struct {
+	uint32_t index, low:31, stack:1;
+	uint32_t i;     // index in gfa_sub_t::v[]; a temporary field
+	uint32_t start; // starting vertex
+} gfa_scinfo_t;
+
+struct gfa_scbuf_s {
+	uint32_t index;
+	gfa_scinfo_t *a;     // node information
+	kvec_t(uint32_t) ts; // Tarjan's stack
+	kvec_t(uint64_t) ds; // DFS stack
+};
+
+gfa_scbuf_t *gfa_scbuf_init(const gfa_t *g)
+{
+	uint32_t v, n_vtx = gfa_n_vtx(g);
+	gfa_scbuf_t *b;
+	GFA_CALLOC(b, 1);
+	GFA_CALLOC(b->a, n_vtx);
+	for (v = 0; v < n_vtx; ++v)
+		b->a[v].index = b->a[v].start = (uint32_t)-1;
+	return b;
+}
+
+void gfa_scbuf_destroy(gfa_scbuf_t *b)
+{
+	free(b->a); free(b->ts.a); free(b->ds.a); free(b);
+}
+
+gfa_sub_t *gfa_scc1(void *km0, const gfa_t *g, gfa_scbuf_t *b, uint32_t v0)
+{
+	gfa_sub_t *sub;
+	uint32_t k, off, m_v = 0;
+
+	KCALLOC(km0, sub, 1);
+	sub->km = km0;
+
+	kv_push(uint64_t, b->ds, (uint64_t)v0<<32);
+	while (b->ds.n > 0) {
+		uint64_t x = kv_pop(b->ds);
+		uint32_t i = (uint32_t)x, v = x>>32, nv;
+		if (i == 0) { // i is the number of outgoing edges already visited
+			b->a[v].low = b->a[v].index = b->index++;
+			b->a[v].stack = 1;
+			kv_push(uint32_t, b->ts, v);
+		}
+		nv = gfa_arc_n(g, v);
+		if (i == nv) { // done with v
+			if (b->a[v].low == b->a[v].index) {
+				int32_t i, j = b->ts.n - 1;
+				while (b->ts.a[j] != v) --j;
+				for (i = b->ts.n - 1; i >= j; --i) {
+					uint32_t w = b->ts.a[i];
+					gfa_subv_t *p;
+					//fprintf(stderr, "V\t%c%s\t%d\t%c%s\t%d\t%d\n", "><"[v&1], g->seg[v>>1].name, i, "><"[w&1], g->seg[w>>1].name, b->a[w^1].stack, b->a[w].index);
+					if (sub->n_v == m_v) KEXPAND(sub->km, sub->v, m_v);
+					p = &sub->v[sub->n_v++];
+					p->v = w;
+					b->a[w].stack = 0;
+				}
+				b->ts.n = j;
+			}
+			if (b->ds.n > 0) { // if the DFS stack is not empty, update the top element
+				uint32_t w = v;
+				v = b->ds.a[b->ds.n - 1] >> 32;
+				b->a[v].low = b->a[v].low < b->a[w].low? b->a[v].low : b->a[w].low;
+			}
+		} else { // process v's neighbor av[i].w
+			gfa_arc_t *av = gfa_arc_a(g, v);
+			uint32_t w = av[i].w;
+			kv_push(uint64_t, b->ds, (uint64_t)v<<32 | (i+1)); // update the old top of the stack
+			if (b->a[w].index == (uint32_t)-1 && b->a[w^1].stack == 0)
+				kv_push(uint64_t, b->ds, (uint64_t)w<<32);
+			else if (b->a[w].stack)
+				b->a[v].low = b->a[v].low < b->a[w].index? b->a[v].low : b->a[w].index;
+		}
+	}
+
+	// reverse the vertex array
+	for (k = 0; k < sub->n_v>>1; ++k) {
+		gfa_subv_t x;
+		x = sub->v[k], sub->v[k] = sub->v[sub->n_v - k - 1], sub->v[sub->n_v - k - 1] = x;
+	}
+
+	// fill other fields in sub
+	for (k = 0; k < sub->n_v; ++k)
+		b->a[sub->v[k].v].start = v0, b->a[sub->v[k].v].i = k;
+	for (k = 0, off = 0; k < sub->n_v; ++k) { // precompute the length of gfa_sub_t::a[]
+		uint32_t v = sub->v[k].v;
+		int32_t i, nv = gfa_arc_n(g, v);
+		gfa_arc_t *av = gfa_arc_a(g, v);
+		for (i = 0; i < nv; ++i)
+			if (b->a[av[i].w].start == v0)
+				++off;
+	}
+	sub->n_a = off;
+	KCALLOC(sub->km, sub->a, sub->n_a);
+	for (k = 0, off = 0; k < sub->n_v; ++k) {
+		uint32_t o0, v = sub->v[k].v;
+		int32_t i, nv = gfa_arc_n(g, v);
+		gfa_arc_t *av = gfa_arc_a(g, v);
+		for (i = 0, o0 = off; i < nv; ++i)
+			if (b->a[av[i].w].start == v0)
+				sub->a[off++] = (uint64_t)b->a[av[i].w].i << 32 | (&av[i] - g->arc);
+		sub->v[k].d = 0;
+		sub->v[k].off = o0;
+		sub->v[k].n = off - o0;
+		if (o0 < off) {
+			radix_sort_gfa64(&sub->a[o0], &sub->a[off]);
+			if (sub->a[o0]>>32 <= k) sub->is_dag = 0;
+		}
+	}
+	return sub;
+}
+
+void gfa_scc_all(const gfa_t *g)
+{
+	uint32_t v, n_vtx = gfa_n_vtx(g);
+	gfa_scbuf_t *b;
+	b = gfa_scbuf_init(g);
+	for (v = 0; v < n_vtx; ++v)
+		if (b->a[v].index == (uint32_t)-1 && b->a[v^1].index == (uint32_t)-1) {
+			gfa_sub_t *sub;
+			sub = gfa_scc1(0, g, b, v);
+			gfa_sub_print(stderr, g, sub);
+			gfa_sub_destroy(sub);
+		}
+	gfa_scbuf_destroy(b);
+}
+
+void gfa_sub_destroy(gfa_sub_t *sub)
+{
+	void *km;
+	if (sub == 0) return;
+	km = sub->km;
+	kfree(km, sub->v); kfree(km, sub->a); kfree(km, sub);
+}
+
+/******************
+ * Bubble calling *
+ ******************/
+
+typedef struct {
+	int32_t ld, sd, rd;
+	int32_t lp, sp;
+	float lf, sf, rf;
+} bb_aux_t;
+
+static void bb_write_seq(const gfa_t *g, int32_t n, const uint32_t *v, int32_t l_seq, char *seq)
+{
+	int32_t k, l;
+	for (k = n - 1, l = 0; k >= 0; --k) {
+		const gfa_seg_t *s = &g->seg[v[k]>>1];
+		if (v[k]&1) {
+			int32_t p;
+			for (p = s->len - 1; p >= 0; --p)
+				seq[l++] = gfa_comp_table[(uint8_t)s->seq[p]];
+		} else {
+			memcpy(&seq[l], s->seq, s->len);
+			l += s->len;
+		}
+	}
+	assert(l == l_seq);
+	seq[l] = 0;
+}
+
+static int32_t bb_n_paths(const gfa_t *g, const gfa_sub_t *sub, int32_t js, int32_t je)
+{
+	int32_t j, k;
+	int64_t *cnt, c;
+	GFA_CALLOC(cnt, je - js + 1);
+	cnt[0] = 1;
+	for (j = js; j < je; ++j) {
+		const gfa_subv_t *t = &sub->v[j];
+		for (k = 0; k < t->n; ++k) {
+			uint64_t a = sub->a[t->off + k];
+			int32_t jv = (int32_t)(a>>32);
+			if (jv <= j || jv > je) continue;
+			if (cnt[jv - js] + cnt[j - js] > INT32_MAX)
+				cnt[jv - js] = INT32_MAX;
+			else cnt[jv - js] += cnt[j - js];
+		}
+	}
+	c = cnt[je - js];
+	free(cnt);
+	return c < INT32_MAX? c : INT32_MAX;
+}
+
+gfa_bubble_t *gfa_bubble(const gfa_t *g, int32_t *n_bb_)
+{
+	uint32_t i, *vs, *vmin, *vtmp = 0;
+	int32_t n_bb = 0, m_bb = 0, m_vtmp = 0;
+	gfa_bubble_t *bb = 0;
+	gfa_scbuf_t *scbuf;
+
+	GFA_MALLOC(vs, g->n_sseq);
+	GFA_MALLOC(vmin, g->n_sseq);
+	for (i = 0; i < g->n_sseq; ++i)
+		vs[i] = (uint32_t)-1, vmin[i] = UINT32_MAX;
+	for (i = 0; i < g->n_seg; ++i) {
+		const gfa_seg_t *s = &g->seg[i];
+		if (s->rank != 0 || s->snid < 0) continue;
+		if ((uint32_t)s->soff < vmin[s->snid])
+			vmin[s->snid] = s->soff, vs[s->snid] = i<<1;
+	}
+	free(vmin);
+
+	scbuf = gfa_scbuf_init(g);
+	for (i = 0; i < g->n_sseq; ++i) {
+		gfa_sub_t *sub;
+		int32_t j, jst, max_a, max_soff;
+		bb_aux_t *ba;
+
+		if (vs[i] == (uint32_t)-1) continue;
+		#if 0
+		sub = gfa_sub_from(0, g, vs[i], 0);
+		#else
+		sub = gfa_scc1(0, g, scbuf, vs[i]);
+		#endif
+		//gfa_sub_print(stderr, g, sub);
+		GFA_CALLOC(ba, sub->n_v);
+		for (j = 0; j < sub->n_v; ++j)
+			ba[j].sd = INT32_MAX, ba[j].lp = ba[j].sp = -1;
+		ba[0].sd = 0;
+		for (j = 0; j < sub->n_v; ++j) {
+			gfa_subv_t *t = &sub->v[j];
+			int32_t k;
+			for (k = 0; k < t->n; ++k) {
+				uint64_t a = sub->a[t->off + k];
+				int32_t jv = (int32_t)(a>>32);
+				int32_t l = (int32_t)g->arc[(uint32_t)a].v_lv;
+				if (jv <= j) continue; // skip loop or cycle
+				if (ba[jv].sd >= ba[j].sd + l)
+					ba[jv].sd = ba[j].sd + l, ba[jv].sp = j;
+				if (ba[jv].ld < ba[j].ld + l)
+					ba[jv].ld = ba[j].ld + l, ba[jv].lp = j;
+			}
+		}
+		for (j = 0, jst = 0, max_a = max_soff = -1; j < sub->n_v; ++j) {
+			gfa_subv_t *t = &sub->v[j];
+			int32_t k;
+			if (j == max_a && g->seg[t->v>>1].soff > max_soff) {
+				const gfa_seg_t *sst = &g->seg[sub->v[jst].v>>1];
+				const gfa_seg_t *sen = &g->seg[t->v>>1];
+				if (sst->snid == i && sen->snid == i) {
+					int32_t n, l;
+					uint32_t *v;
+					gfa_bubble_t *b;
+
+					// basic information
+					if (n_bb == m_bb) GFA_EXPAND(bb, m_bb);
+					b = &bb[n_bb++];
+					b->snid = i;
+					b->vs = sub->v[jst].v;
+					b->ve = t->v;
+					b->ss = sst->soff + sst->len;
+					b->se = sen->soff;
+					b->len_min = ba[j].sd - ba[jst].sd - sst->len;
+					b->len_max = ba[j].ld - ba[jst].ld - sst->len;
+					b->n_paths = bb_n_paths(g, sub, jst, j);
+					//fprintf(stderr, "X\t%s[%d]\tvs=%c%s\tve=%c%s\tlen_min=%d\n", g->sseq[i].name, i, "><"[b->vs&1], g->seg[b->vs>>1].name, "><"[b->ve&1], g->seg[b->ve>>1].name, b->len_min);
+					assert(b->len_min >= 0);
+					assert(b->len_max >= 0 && b->len_max >= b->len_min);
+					b->n_seg = j - jst + 1;
+					l = (b->len_min + 1) + (b->len_max + 1);
+					l = (l + 3) / 4 + b->n_seg;
+					GFA_CALLOC(b->v, l);
+					b->seq_min = (char*)(b->v + b->n_seg);
+					b->seq_max = b->seq_min + b->len_min + 1;
+					for (k = jst; k <= j; ++k)
+						b->v[k - jst] = sub->v[k].v;
+
+					// test bubble involving both strands (mostly inversions)
+					if (b->n_seg > m_vtmp) {
+						m_vtmp = b->n_seg;
+						kroundup32(m_vtmp);
+						GFA_REALLOC(vtmp, m_vtmp);
+					}
+					for (k = 0; k < b->n_seg; ++k) vtmp[k] = b->v[k]>>1;
+					radix_sort_gfa32(vtmp, vtmp + b->n_seg);
+					for (k = 1; k < b->n_seg; ++k)
+						if (vtmp[k] == vtmp[k-1]) break;
+					b->is_bidir = (k < b->n_seg);
+
+					// generate sequences and cf_min/cf_max
+					GFA_MALLOC(v, j - jst);
+					k = j, n = 0;
+					while (k > jst) {
+						if (k < j) v[n++] = sub->v[k].v;
+						k = ba[k].sp;
+					}
+					bb_write_seq(g, n, v, b->len_min, b->seq_min);
+					k = j, n = 0;
+					while (k > jst) {
+						if (k < j) v[n++] = sub->v[k].v;
+						k = ba[k].lp;
+					}
+					bb_write_seq(g, n, v, b->len_max, b->seq_max);
+					free(v);
+				} // ~if(sst->snid==i&&sen->snid==i)
+				max_a = max_soff = -1, jst = j;
+			} // ~if(j==max_a)
+			for (k = 0; k < t->n; ++k)
+				if ((int32_t)(sub->a[t->off + k]>>32) > max_a)
+					max_a = sub->a[t->off + k]>>32;
+			if (g->seg[t->v>>1].snid == i && g->seg[t->v>>1].soff > max_soff)
+				max_soff = g->seg[t->v>>1].soff;
+		}
+		free(ba);
+		gfa_sub_destroy(sub);
+	}
+	free(vtmp);
+	gfa_scbuf_destroy(scbuf);
+	free(vs);
+	*n_bb_ = n_bb;
+	return bb;
+}