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assembly.h
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27 
28 #pragma once
29 
30 #include <nvbio/basic/types.h>
31 #include <nvbio/basic/vector.h>
33 
34 #include "haplotype_caller.h"
35 #include "assembly_types.h"
36 
37 using namespace nvbio;
38 
40 {
41  // [read correction]
42 
43  // create assembly graphs for given kmer size(s)
44  debruijn_graph assembly_graph;
45  assembly_graph.construct_graph(
46  pipeline->d_seq_set,
47  pipeline->d_active_region_ids,
48  pipeline->kmer_size,
49  false);
50 
51  printf("Constructed assembly graph for kmer size %u with %u nodes and %u edges \n",
52  pipeline->kmer_size, assembly_graph.n_nodes, assembly_graph.n_edges);
53 
54  //assembly_graph.print_dot_graph(pipeline->d_seq_set);
55 
56  // check complexity
57 
58  // assembly_graph.topological_sort();
59 
60  // check for cycles
61  // post-process: pruning, dangling chain recovery...
62 
63  // find best paths
64  //assembly_graph.find_k_best_paths(pipeline->k_best_haplotypes);
65 }