ruby-minigraph 0.0.20.0
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- checksums.yaml +7 -0
- data/LICENSE.txt +21 -0
- data/README.md +62 -0
- data/ext/Rakefile +56 -0
- data/ext/cmappy/cmappy.c +7 -0
- data/ext/cmappy/cmappy.h +8 -0
- data/ext/minigraph/LICENSE.txt +23 -0
- data/ext/minigraph/Makefile +66 -0
- data/ext/minigraph/NEWS.md +317 -0
- data/ext/minigraph/README.md +207 -0
- data/ext/minigraph/algo.c +194 -0
- data/ext/minigraph/algo.h +33 -0
- data/ext/minigraph/asm-call.c +147 -0
- data/ext/minigraph/bseq.c +133 -0
- data/ext/minigraph/bseq.h +76 -0
- data/ext/minigraph/cal_cov.c +139 -0
- data/ext/minigraph/doc/example1.png +0 -0
- data/ext/minigraph/doc/example2.png +0 -0
- data/ext/minigraph/doc/examples.graffle +0 -0
- data/ext/minigraph/format.c +241 -0
- data/ext/minigraph/galign.c +140 -0
- data/ext/minigraph/gchain1.c +532 -0
- data/ext/minigraph/gcmisc.c +223 -0
- data/ext/minigraph/gfa-aug.c +260 -0
- data/ext/minigraph/gfa-base.c +526 -0
- data/ext/minigraph/gfa-bbl.c +372 -0
- data/ext/minigraph/gfa-ed.c +617 -0
- data/ext/minigraph/gfa-io.c +395 -0
- data/ext/minigraph/gfa-priv.h +154 -0
- data/ext/minigraph/gfa.h +166 -0
- data/ext/minigraph/ggen.c +182 -0
- data/ext/minigraph/ggen.h +21 -0
- data/ext/minigraph/ggsimple.c +570 -0
- data/ext/minigraph/gmap.c +211 -0
- data/ext/minigraph/index.c +230 -0
- data/ext/minigraph/kalloc.c +224 -0
- data/ext/minigraph/kalloc.h +82 -0
- data/ext/minigraph/kavl.h +414 -0
- data/ext/minigraph/kdq.h +134 -0
- data/ext/minigraph/ketopt.h +116 -0
- data/ext/minigraph/khashl.h +348 -0
- data/ext/minigraph/krmq.h +474 -0
- data/ext/minigraph/kseq.h +256 -0
- data/ext/minigraph/ksort.h +164 -0
- data/ext/minigraph/kstring.h +165 -0
- data/ext/minigraph/kthread.c +159 -0
- data/ext/minigraph/kthread.h +15 -0
- data/ext/minigraph/kvec-km.h +105 -0
- data/ext/minigraph/kvec.h +110 -0
- data/ext/minigraph/lchain.c +441 -0
- data/ext/minigraph/main.c +301 -0
- data/ext/minigraph/map-algo.c +500 -0
- data/ext/minigraph/mgpriv.h +128 -0
- data/ext/minigraph/minigraph.1 +359 -0
- data/ext/minigraph/minigraph.h +176 -0
- data/ext/minigraph/miniwfa.c +834 -0
- data/ext/minigraph/miniwfa.h +95 -0
- data/ext/minigraph/misc/mgutils.js +1451 -0
- data/ext/minigraph/misc.c +12 -0
- data/ext/minigraph/options.c +134 -0
- data/ext/minigraph/shortk.c +251 -0
- data/ext/minigraph/sketch.c +109 -0
- data/ext/minigraph/sys.c +147 -0
- data/ext/minigraph/sys.h +20 -0
- data/ext/minigraph/test/MT-chimp.fa +277 -0
- data/ext/minigraph/test/MT-human.fa +239 -0
- data/ext/minigraph/test/MT-orangA.fa +276 -0
- data/ext/minigraph/test/MT.gfa +19 -0
- data/ext/minigraph/tex/Makefile +13 -0
- data/ext/minigraph/tex/minigraph.bib +676 -0
- data/ext/minigraph/tex/minigraph.tex +986 -0
- data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.gp +42 -0
- data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.tbl +13 -0
- data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.gp +269 -0
- data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.sh +7 -0
- data/ext/minigraph/tex/plots/CHM13v1.cen.bed +23 -0
- data/ext/minigraph/tex/plots/CHM13v1.size +23 -0
- data/ext/minigraph/tex/plots/anno2tbl.js +40 -0
- data/ext/minigraph/tex/plots/bedutils.js +367 -0
- data/ext/minigraph/tex/plots/chr-plot.js +130 -0
- data/ext/minigraph/tex/plots/gen-anno.mak +24 -0
- data/ext/minigraph.patch +21 -0
- data/lib/minigraph/ffi/constants.rb +230 -0
- data/lib/minigraph/ffi/functions.rb +70 -0
- data/lib/minigraph/ffi/mappy.rb +8 -0
- data/lib/minigraph/ffi.rb +27 -0
- data/lib/minigraph/version.rb +5 -0
- data/lib/minigraph.rb +72 -0
- metadata +159 -0
@@ -0,0 +1,372 @@
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#include <assert.h>
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#include <stdio.h>
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#include "gfa-priv.h"
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#include "kalloc.h"
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#include "ksort.h"
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#include "kvec.h"
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#define generic_key(x) (x)
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KRADIX_SORT_INIT(gfa32, uint32_t, generic_key, 4)
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void gfa_sort_ref_arc(gfa_t *g)
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{
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uint32_t v, n_vtx = gfa_n_vtx(g);
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for (v = 0; v < n_vtx; ++v) {
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gfa_seg_t *s = &g->seg[v>>1];
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int32_t i, nv;
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gfa_arc_t *av, b;
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if (s->rank != 0) continue;
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nv = gfa_arc_n(g, v);
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av = gfa_arc_a(g, v);
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for (i = 0; i < nv; ++i) {
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uint32_t w = av[i].w;
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gfa_seg_t *t = &g->seg[w>>1];
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if (t->rank == 0 && t->snid == s->snid && (v&1) == (w&1)) {
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if (((v&1) == 0 && s->soff + s->len == t->soff) || ((v&1) == 1 && t->soff + t->len == s->soff))
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break;
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}
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}
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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);
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assert(nv == 0 || i < nv);
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if (i > 0 && i < nv) b = av[i], av[i] = av[0], av[0] = b;
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}
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}
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void gfa_sub_print(FILE *fp, const gfa_t *g, const gfa_sub_t *sub)
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{
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int32_t i, j;
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for (i = 0; i < sub->n_v; ++i) {
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gfa_subv_t *p = &sub->v[i];
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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);
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if (p->n > 0) {
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fputc('\t', fp);
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for (j = 0; j < p->n; ++j) {
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if (j) fputc(',', fp);
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fprintf(fp, "%d", (uint32_t)(sub->a[p->off + j]>>32));
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}
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}
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fputc('\n', fp);
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}
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}
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/****************
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* Tarjan's SCC *
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****************/
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typedef struct {
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uint32_t index, low:31, stack:1;
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uint32_t i; // index in gfa_sub_t::v[]; a temporary field
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uint32_t start; // starting vertex
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} gfa_scinfo_t;
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struct gfa_scbuf_s {
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uint32_t index;
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gfa_scinfo_t *a; // node information
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kvec_t(uint32_t) ts; // Tarjan's stack
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kvec_t(uint64_t) ds; // DFS stack
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};
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gfa_scbuf_t *gfa_scbuf_init(const gfa_t *g)
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{
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uint32_t v, n_vtx = gfa_n_vtx(g);
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gfa_scbuf_t *b;
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GFA_CALLOC(b, 1);
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GFA_CALLOC(b->a, n_vtx);
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for (v = 0; v < n_vtx; ++v)
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b->a[v].index = b->a[v].start = (uint32_t)-1;
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return b;
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}
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void gfa_scbuf_destroy(gfa_scbuf_t *b)
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{
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free(b->a); free(b->ts.a); free(b->ds.a); free(b);
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}
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gfa_sub_t *gfa_scc1(void *km0, const gfa_t *g, gfa_scbuf_t *b, uint32_t v0)
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{
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gfa_sub_t *sub;
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uint32_t k, off, m_v = 0;
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KCALLOC(km0, sub, 1);
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sub->km = km0;
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kv_push(uint64_t, b->ds, (uint64_t)v0<<32);
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while (b->ds.n > 0) {
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uint64_t x = kv_pop(b->ds);
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uint32_t i = (uint32_t)x, v = x>>32, nv;
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if (i == 0) { // i is the number of outgoing edges already visited
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b->a[v].low = b->a[v].index = b->index++;
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b->a[v].stack = 1;
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kv_push(uint32_t, b->ts, v);
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}
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nv = gfa_arc_n(g, v);
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if (i == nv) { // done with v
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if (b->a[v].low == b->a[v].index) {
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int32_t i, j = b->ts.n - 1;
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while (b->ts.a[j] != v) --j;
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for (i = b->ts.n - 1; i >= j; --i) {
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uint32_t w = b->ts.a[i];
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gfa_subv_t *p;
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//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);
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if (sub->n_v == m_v) KEXPAND(sub->km, sub->v, m_v);
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p = &sub->v[sub->n_v++];
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p->v = w;
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b->a[w].stack = 0;
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}
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b->ts.n = j;
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}
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if (b->ds.n > 0) { // if the DFS stack is not empty, update the top element
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uint32_t w = v;
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v = b->ds.a[b->ds.n - 1] >> 32;
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b->a[v].low = b->a[v].low < b->a[w].low? b->a[v].low : b->a[w].low;
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}
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} else { // process v's neighbor av[i].w
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gfa_arc_t *av = gfa_arc_a(g, v);
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uint32_t w = av[i].w;
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kv_push(uint64_t, b->ds, (uint64_t)v<<32 | (i+1)); // update the old top of the stack
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if (b->a[w].index == (uint32_t)-1 && b->a[w^1].stack == 0)
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kv_push(uint64_t, b->ds, (uint64_t)w<<32);
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else if (b->a[w].stack)
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b->a[v].low = b->a[v].low < b->a[w].index? b->a[v].low : b->a[w].index;
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}
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}
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// reverse the vertex array
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for (k = 0; k < sub->n_v>>1; ++k) {
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gfa_subv_t x;
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x = sub->v[k], sub->v[k] = sub->v[sub->n_v - k - 1], sub->v[sub->n_v - k - 1] = x;
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}
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// fill other fields in sub
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for (k = 0; k < sub->n_v; ++k)
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b->a[sub->v[k].v].start = v0, b->a[sub->v[k].v].i = k;
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for (k = 0, off = 0; k < sub->n_v; ++k) { // precompute the length of gfa_sub_t::a[]
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uint32_t v = sub->v[k].v;
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int32_t i, nv = gfa_arc_n(g, v);
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gfa_arc_t *av = gfa_arc_a(g, v);
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for (i = 0; i < nv; ++i)
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if (b->a[av[i].w].start == v0)
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++off;
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}
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sub->n_a = off;
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KCALLOC(sub->km, sub->a, sub->n_a);
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for (k = 0, off = 0; k < sub->n_v; ++k) {
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uint32_t o0, v = sub->v[k].v;
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int32_t i, nv = gfa_arc_n(g, v);
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gfa_arc_t *av = gfa_arc_a(g, v);
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for (i = 0, o0 = off; i < nv; ++i)
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if (b->a[av[i].w].start == v0)
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sub->a[off++] = (uint64_t)b->a[av[i].w].i << 32 | (&av[i] - g->arc);
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sub->v[k].d = 0;
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sub->v[k].off = o0;
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sub->v[k].n = off - o0;
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if (o0 < off) {
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radix_sort_gfa64(&sub->a[o0], &sub->a[off]);
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if (sub->a[o0]>>32 <= k) sub->is_dag = 0;
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}
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}
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return sub;
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}
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void gfa_scc_all(const gfa_t *g)
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{
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uint32_t v, n_vtx = gfa_n_vtx(g);
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gfa_scbuf_t *b;
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b = gfa_scbuf_init(g);
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for (v = 0; v < n_vtx; ++v)
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if (b->a[v].index == (uint32_t)-1 && b->a[v^1].index == (uint32_t)-1) {
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gfa_sub_t *sub;
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sub = gfa_scc1(0, g, b, v);
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gfa_sub_print(stderr, g, sub);
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gfa_sub_destroy(sub);
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}
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gfa_scbuf_destroy(b);
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}
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void gfa_sub_destroy(gfa_sub_t *sub)
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{
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void *km;
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if (sub == 0) return;
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km = sub->km;
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191
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kfree(km, sub->v); kfree(km, sub->a); kfree(km, sub);
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192
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}
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/******************
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195
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* Bubble calling *
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196
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******************/
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197
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198
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typedef struct {
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199
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int32_t ld, sd, rd;
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200
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int32_t lp, sp;
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201
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float lf, sf, rf;
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} bb_aux_t;
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static void bb_write_seq(const gfa_t *g, int32_t n, const uint32_t *v, int32_t l_seq, char *seq)
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{
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206
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int32_t k, l;
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for (k = n - 1, l = 0; k >= 0; --k) {
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208
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const gfa_seg_t *s = &g->seg[v[k]>>1];
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209
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if (v[k]&1) {
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int32_t p;
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211
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for (p = s->len - 1; p >= 0; --p)
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212
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seq[l++] = gfa_comp_table[(uint8_t)s->seq[p]];
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213
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} else {
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214
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memcpy(&seq[l], s->seq, s->len);
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215
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l += s->len;
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216
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}
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217
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}
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218
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assert(l == l_seq);
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219
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seq[l] = 0;
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220
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}
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221
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222
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static int32_t bb_n_paths(const gfa_t *g, const gfa_sub_t *sub, int32_t js, int32_t je)
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223
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{
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224
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int32_t j, k;
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225
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int64_t *cnt, c;
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226
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GFA_CALLOC(cnt, je - js + 1);
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227
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cnt[0] = 1;
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228
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for (j = js; j < je; ++j) {
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const gfa_subv_t *t = &sub->v[j];
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230
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for (k = 0; k < t->n; ++k) {
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uint64_t a = sub->a[t->off + k];
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int32_t jv = (int32_t)(a>>32);
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233
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if (jv <= j || jv > je) continue;
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234
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if (cnt[jv - js] + cnt[j - js] > INT32_MAX)
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235
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cnt[jv - js] = INT32_MAX;
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236
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else cnt[jv - js] += cnt[j - js];
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237
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}
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238
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}
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239
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c = cnt[je - js];
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240
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free(cnt);
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241
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return c < INT32_MAX? c : INT32_MAX;
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242
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+
}
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243
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244
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+
gfa_bubble_t *gfa_bubble(const gfa_t *g, int32_t *n_bb_)
|
245
|
+
{
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246
|
+
uint32_t i, *vs, *vmin, *vtmp = 0;
|
247
|
+
int32_t n_bb = 0, m_bb = 0, m_vtmp = 0;
|
248
|
+
gfa_bubble_t *bb = 0;
|
249
|
+
gfa_scbuf_t *scbuf;
|
250
|
+
|
251
|
+
GFA_MALLOC(vs, g->n_sseq);
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252
|
+
GFA_MALLOC(vmin, g->n_sseq);
|
253
|
+
for (i = 0; i < g->n_sseq; ++i)
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254
|
+
vs[i] = (uint32_t)-1, vmin[i] = UINT32_MAX;
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255
|
+
for (i = 0; i < g->n_seg; ++i) {
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256
|
+
const gfa_seg_t *s = &g->seg[i];
|
257
|
+
if (s->rank != 0 || s->snid < 0) continue;
|
258
|
+
if ((uint32_t)s->soff < vmin[s->snid])
|
259
|
+
vmin[s->snid] = s->soff, vs[s->snid] = i<<1;
|
260
|
+
}
|
261
|
+
free(vmin);
|
262
|
+
|
263
|
+
scbuf = gfa_scbuf_init(g);
|
264
|
+
for (i = 0; i < g->n_sseq; ++i) {
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265
|
+
gfa_sub_t *sub;
|
266
|
+
int32_t j, jst, max_a, max_soff;
|
267
|
+
bb_aux_t *ba;
|
268
|
+
|
269
|
+
if (vs[i] == (uint32_t)-1) continue;
|
270
|
+
#if 0
|
271
|
+
sub = gfa_sub_from(0, g, vs[i], 0);
|
272
|
+
#else
|
273
|
+
sub = gfa_scc1(0, g, scbuf, vs[i]);
|
274
|
+
#endif
|
275
|
+
//gfa_sub_print(stderr, g, sub);
|
276
|
+
GFA_CALLOC(ba, sub->n_v);
|
277
|
+
for (j = 0; j < sub->n_v; ++j)
|
278
|
+
ba[j].sd = INT32_MAX, ba[j].lp = ba[j].sp = -1;
|
279
|
+
ba[0].sd = 0;
|
280
|
+
for (j = 0; j < sub->n_v; ++j) {
|
281
|
+
gfa_subv_t *t = &sub->v[j];
|
282
|
+
int32_t k;
|
283
|
+
for (k = 0; k < t->n; ++k) {
|
284
|
+
uint64_t a = sub->a[t->off + k];
|
285
|
+
int32_t jv = (int32_t)(a>>32);
|
286
|
+
int32_t l = (int32_t)g->arc[(uint32_t)a].v_lv;
|
287
|
+
if (jv <= j) continue; // skip loop or cycle
|
288
|
+
if (ba[jv].sd >= ba[j].sd + l)
|
289
|
+
ba[jv].sd = ba[j].sd + l, ba[jv].sp = j;
|
290
|
+
if (ba[jv].ld < ba[j].ld + l)
|
291
|
+
ba[jv].ld = ba[j].ld + l, ba[jv].lp = j;
|
292
|
+
}
|
293
|
+
}
|
294
|
+
for (j = 0, jst = 0, max_a = max_soff = -1; j < sub->n_v; ++j) {
|
295
|
+
gfa_subv_t *t = &sub->v[j];
|
296
|
+
int32_t k;
|
297
|
+
if (j == max_a && g->seg[t->v>>1].soff > max_soff) {
|
298
|
+
const gfa_seg_t *sst = &g->seg[sub->v[jst].v>>1];
|
299
|
+
const gfa_seg_t *sen = &g->seg[t->v>>1];
|
300
|
+
if (sst->snid == i && sen->snid == i) {
|
301
|
+
int32_t n, l;
|
302
|
+
uint32_t *v;
|
303
|
+
gfa_bubble_t *b;
|
304
|
+
|
305
|
+
// basic information
|
306
|
+
if (n_bb == m_bb) GFA_EXPAND(bb, m_bb);
|
307
|
+
b = &bb[n_bb++];
|
308
|
+
b->snid = i;
|
309
|
+
b->vs = sub->v[jst].v;
|
310
|
+
b->ve = t->v;
|
311
|
+
b->ss = sst->soff + sst->len;
|
312
|
+
b->se = sen->soff;
|
313
|
+
b->len_min = ba[j].sd - ba[jst].sd - sst->len;
|
314
|
+
b->len_max = ba[j].ld - ba[jst].ld - sst->len;
|
315
|
+
b->n_paths = bb_n_paths(g, sub, jst, j);
|
316
|
+
//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);
|
317
|
+
assert(b->len_min >= 0);
|
318
|
+
assert(b->len_max >= 0 && b->len_max >= b->len_min);
|
319
|
+
b->n_seg = j - jst + 1;
|
320
|
+
l = (b->len_min + 1) + (b->len_max + 1);
|
321
|
+
l = (l + 3) / 4 + b->n_seg;
|
322
|
+
GFA_CALLOC(b->v, l);
|
323
|
+
b->seq_min = (char*)(b->v + b->n_seg);
|
324
|
+
b->seq_max = b->seq_min + b->len_min + 1;
|
325
|
+
for (k = jst; k <= j; ++k)
|
326
|
+
b->v[k - jst] = sub->v[k].v;
|
327
|
+
|
328
|
+
// test bubble involving both strands (mostly inversions)
|
329
|
+
if (b->n_seg > m_vtmp) {
|
330
|
+
m_vtmp = b->n_seg;
|
331
|
+
kroundup32(m_vtmp);
|
332
|
+
GFA_REALLOC(vtmp, m_vtmp);
|
333
|
+
}
|
334
|
+
for (k = 0; k < b->n_seg; ++k) vtmp[k] = b->v[k]>>1;
|
335
|
+
radix_sort_gfa32(vtmp, vtmp + b->n_seg);
|
336
|
+
for (k = 1; k < b->n_seg; ++k)
|
337
|
+
if (vtmp[k] == vtmp[k-1]) break;
|
338
|
+
b->is_bidir = (k < b->n_seg);
|
339
|
+
|
340
|
+
// generate sequences and cf_min/cf_max
|
341
|
+
GFA_MALLOC(v, j - jst);
|
342
|
+
k = j, n = 0;
|
343
|
+
while (k > jst) {
|
344
|
+
if (k < j) v[n++] = sub->v[k].v;
|
345
|
+
k = ba[k].sp;
|
346
|
+
}
|
347
|
+
bb_write_seq(g, n, v, b->len_min, b->seq_min);
|
348
|
+
k = j, n = 0;
|
349
|
+
while (k > jst) {
|
350
|
+
if (k < j) v[n++] = sub->v[k].v;
|
351
|
+
k = ba[k].lp;
|
352
|
+
}
|
353
|
+
bb_write_seq(g, n, v, b->len_max, b->seq_max);
|
354
|
+
free(v);
|
355
|
+
} // ~if(sst->snid==i&&sen->snid==i)
|
356
|
+
max_a = max_soff = -1, jst = j;
|
357
|
+
} // ~if(j==max_a)
|
358
|
+
for (k = 0; k < t->n; ++k)
|
359
|
+
if ((int32_t)(sub->a[t->off + k]>>32) > max_a)
|
360
|
+
max_a = sub->a[t->off + k]>>32;
|
361
|
+
if (g->seg[t->v>>1].snid == i && g->seg[t->v>>1].soff > max_soff)
|
362
|
+
max_soff = g->seg[t->v>>1].soff;
|
363
|
+
}
|
364
|
+
free(ba);
|
365
|
+
gfa_sub_destroy(sub);
|
366
|
+
}
|
367
|
+
free(vtmp);
|
368
|
+
gfa_scbuf_destroy(scbuf);
|
369
|
+
free(vs);
|
370
|
+
*n_bb_ = n_bb;
|
371
|
+
return bb;
|
372
|
+
}
|