示例#1
0
 /**
  * Write the read if it matches and then pass it down the chain if
  * appropriate.
  */
 void readMatch(bool matches,
                std::shared_ptr<bam_hdr_t> &header,
                std::shared_ptr<bam1_t> &read) {
   if (matches) {
     count++;
     if (output_file) {
       sam_write1(output_file.get(), header.get(), read.get());
     }
   }
   if (next && checkChain(chain, matches)) {
     next->processRead(header, read);
   }
 }
示例#2
0
 /**
  * We want this chromosome if our query is interested or the next link can
  * make use of it _if_ it will see it upon failure (otherwise, its behaviour
  * is determined by ours.
  */
 bool wantChromosome(std::shared_ptr<bam_hdr_t> &header, uint32_t tid) {
   return CheckIterator::wantChromosome(header, tid) ||
          next && checkChain(chain, false) &&
              next->wantChromosome(header, tid);
 }
示例#3
0
/* makeGraphs:
 * Generate dags modeling the row and column constraints.
 * If the table has cc columns, we create the graph
 *  0 -> 1 -> 2 -> ... -> cc
 * and if a cell starts in column c with span cspan, with
 * width w, we add the edge c -> c+cspan [minlen = w].
 *
 * We might simplify the graph by removing multiedges,
 * using the max minlen, but will affect the balancing?
 */
void makeGraphs(htmltbl_t * tbl, graph_t * rowg, graph_t * colg)
{
    htmlcell_t *cp;
    htmlcell_t **cells;
    node_t *t;
    node_t *lastn;
    node_t *h;
    edge_t *e;
    int i;
    int* minc;
    int* minr;

    lastn = NULL;
    for (i = 0; i <= tbl->cc; i++) {
	t = agnode(colg, nToName(i));
	alloc_elist(tbl->rc, ND_in(t));
	alloc_elist(tbl->rc, ND_out(t));
	if (lastn) {
	    ND_next(lastn) = t;
	    lastn = t;
	} else {
	    lastn = GD_nlist(colg) = t;
	}
    }
    lastn = NULL;
    for (i = 0; i <= tbl->rc; i++) {
	t = agnode(rowg, nToName(i));
	alloc_elist(tbl->cc, ND_in(t));
	alloc_elist(tbl->cc, ND_out(t));
	if (lastn) {
	    ND_next(lastn) = t;
	    lastn = t;
	} else {
	    lastn = GD_nlist(rowg) = t;
	}
    }
    minr = N_NEW(tbl->rc, int);
    minc = N_NEW(tbl->cc, int);
    for (cells = tbl->u.n.cells; *cells; cells++) {
        int x, y, c, r;
	cp = *cells;
        x = (cp->data.box.UR.x + (cp->cspan-1))/cp->cspan;
        for (c = 0; c < cp->cspan; c++)
          minc[cp->col + c] = MAX(minc[cp->col + c],x);
        y = (cp->data.box.UR.y + (cp->rspan-1))/cp->rspan;
        for (r = 0; r < cp->rspan; r++)
          minr[cp->row + r] = MAX(minr[cp->row + r],y);
    }
    for (cells = tbl->u.n.cells; *cells; cells++) {
        int x, y, c, r;
	cp = *cells;
	t = agfindnode(colg, nToName(cp->col));
	h = agfindnode(colg, nToName(cp->col + cp->cspan));
	e = agedge(colg, t, h);
        x = 0;
        for (c = 0; c < cp->cspan; c++)
            x += minc[cp->col + c];
	ED_minlen(e) = x;
	/* ED_minlen(e) = cp->data.box.UR.x; */
#ifdef DEBUG
	fprintf(stderr, "col edge %s -> %s %d\n", t->name, h->name,
		ED_minlen(e));
#endif
	elist_append(e, ND_out(t));
	elist_append(e, ND_in(h));

	t = agfindnode(rowg, nToName(cp->row));
	h = agfindnode(rowg, nToName(cp->row + cp->rspan));
	e = agedge(rowg, t, h);
        y = 0;
        for (r = 0; r < cp->rspan; r++)
            y += minr[cp->row + r];
	ED_minlen(e) = y;
	/* ED_minlen(e) = cp->data.box.UR.y; */
#ifdef DEBUG
	fprintf(stderr, "row edge %s -> %s %d\n", t->name, h->name,
		ED_minlen(e));
#endif
	elist_append(e, ND_out(t));
	elist_append(e, ND_in(h));
    }

    /* Make sure that 0 <= 1 <= 2 ...k. This implies graph connected. */
    checkChain(colg);
    checkChain(rowg);

    free (minc);
    free (minr);
}