C++ (Cpp) find_bubbles_ending_with 예제들

예제 #1

파일: bubble_caller_tests.c 프로젝트: Phelimb/mccortex

// `nbuf` and `sbuf` are temporary variables used by this function
static void _call_bubble(BubbleCaller *caller,
                         const char *flank5p, const char *flank3p,
                         const char **alleles, size_t num_alleles,
                         dBNodeBuffer *nbuf, StrBuf *sbuf)
{
  const dBGraph *graph = caller->db_graph;
  const size_t kmer_size = graph->kmer_size;

  dBNode node5p = db_graph_find_str(graph, flank5p+strlen(flank5p)-kmer_size);
  dBNode node3p = db_graph_find_str(graph, flank3p);
  TASSERT(node5p.key != HASH_NOT_FOUND);
  TASSERT(node3p.key != HASH_NOT_FOUND);

  Edges edges5p = db_node_get_edges_union(graph, node5p.key);
  Edges edges3p = db_node_get_edges_union(graph, node3p.key);
  TASSERT(edges_get_outdegree(edges5p, node5p.orient) > 1);
  TASSERT(edges_get_indegree(edges3p, node3p.orient) > 1);

  find_bubbles(caller, node5p);

  GCacheUnitig *snode3p;
  Orientation snorient3p;
  GCacheStepPtrBuf *stepbuf;

  // Get 3p flank and orientation
  snode3p = graph_cache_find_unitig(&caller->cache, node3p);
  TASSERT(snode3p != NULL);
  snorient3p = gc_unitig_get_orient(&caller->cache, snode3p, node3p);

  find_bubbles_ending_with(caller, snode3p);

  stepbuf = (snorient3p == FORWARD ? &caller->spp_forward : &caller->spp_reverse);

  _check_alleles(&caller->cache, stepbuf, alleles, num_alleles, nbuf, sbuf);
}

예제 #2

파일: bubble_caller.c 프로젝트: ambarrio/mccortex

static void write_bubbles_to_file(BubbleCaller *caller)
{
  // Loop over supernodes checking if they are 3p flanks
  size_t snode_count = graph_cache_num_snodes(&caller->cache);
  GCacheSnode *snode;
  size_t i;

  for(i = 0; i < snode_count; i++)
  {
    snode = graph_cache_snode(&caller->cache, i);
    find_bubbles_ending_with(caller, snode);

    if(caller->spp_forward.len > 1)
      print_bubble(caller, caller->spp_forward.b, caller->spp_forward.len);
    if(caller->spp_reverse.len > 1)
      print_bubble(caller, caller->spp_reverse.b, caller->spp_reverse.len);
  }
}