delete multi-arcs * remove edges like: v has two out-edges to w **/

in a resolved bubble, mark unused vertices and arcs as "reduced"

pop bubbles from vertex v0; the graph MJUST BE symmetric: if u->v present, v'->u' must be present as well note!!!!!!!! here we don't exculde the delet

pop bubbles from vertex v0; the graph MJUST BE symmetric: if u->v present, v'->u' must be present as well note!!!!!!!! here we don't exculde the delet

ai > aj

double band_width_threshold = 0.05;

no e_end since e always covers end; s may not have end

ai[].x: ref_id(31)rev(1)r_pos(32) ai[].y: weight(8)query_id(8)flag(8)span(8)q_pos(32) comput_sc(&a[i], &a[j], max_dist_x, max_dist_y, bw, chn_pen_gap,

count the number of outgoing arcs, including reduced arcs

count the number of outgoing arcs, including reduced arcs

to delete a node 1. set the corresponding base to be 'D' 2. remove all related edges 2. clear all related edges 3. g_nodes.delete_length++, please do