float ReferenceGraph::adjudicateAlignment(std::shared_ptr< BamTools::BamAlignment > bamAlignmentPtr, Sample::SharedPtr samplePtr, uint32_t matchValue, uint32_t mismatchValue, uint32_t gapOpenValue, uint32_t gapExtensionValue)
{
gssw_sse2_disable();
int8_t* nt_table = gssw_create_nt_table();
int8_t* mat = gssw_create_score_matrix(matchValue, mismatchValue);
gssw_graph* graph = gssw_graph_create(1);
gssw_node* gsswNode = (gssw_node*)gssw_node_create(m_node.get(), m_node->getID(), m_node->getSequence().c_str(), nt_table, mat);
gssw_graph_add_node(graph, gsswNode);
gssw_graph_fill(graph, bamAlignmentPtr->QueryBases.c_str(), nt_table, mat, gapOpenValue, gapExtensionValue, 0, 0, 15, 2, true);
gssw_graph_mapping* gm = gssw_graph_trace_back (graph, bamAlignmentPtr->QueryBases.c_str(), bamAlignmentPtr->QueryBases.size(), nt_table, mat, gapOpenValue, gapExtensionValue, 0, 0);
float swPercent = processTraceback(gm, bamAlignmentPtr, samplePtr, !bamAlignmentPtr->IsReverseStrand(), matchValue, mismatchValue, gapOpenValue, gapExtensionValue);
gssw_graph_mapping_destroy(gm);
// note that nodes which are referred to in this graph are destroyed as well
gssw_graph_destroy(graph);
free(nt_table);
free(mat);
return swPercent;
}
// Align a pair of genome sequences.
int main (int argc, char * const argv[]) {
// default parameters for genome sequence alignment
int32_t match = 2, mismatch = 2, gap_open = 3, gap_extension = 1;
// from Mengyao's example about the importance of using all three matrices in traceback.
// int32_t l, m, k, match = 2, mismatch = 1, gap_open = 2, gap_extension = 1;
char *ref_seq_1 = argv[1];
char *ref_seq_2 = argv[2];
char *ref_seq_3 = argv[3];
char *ref_seq_4 = argv[4];
char *read_seq = argv[5];
/* This table is used to transform nucleotide letters into numbers. */
int8_t* nt_table = gssw_create_nt_table();
// initialize scoring matrix for genome sequences
// A C G T N (or other ambiguous code)
// 2 -2 -2 -2 0 A
// -2 2 -2 -2 0 C
// -2 -2 2 -2 0 G
// -2 -2 -2 2 0 T
// 0 0 0 0 0 N (or other ambiguous code)
int8_t* mat = gssw_create_score_matrix(match, mismatch);
gssw_node* nodes[4];
nodes[0] = (gssw_node*)gssw_node_create("A", 1, ref_seq_1, nt_table, mat);
nodes[1] = (gssw_node*)gssw_node_create("B", 2, ref_seq_2, nt_table, mat);
nodes[2] = (gssw_node*)gssw_node_create("C", 3, ref_seq_3, nt_table, mat);
nodes[3] = (gssw_node*)gssw_node_create("D", 4, ref_seq_4, nt_table, mat);
// makes a diamond
gssw_nodes_add_edge(nodes[0], nodes[1]);
gssw_nodes_add_edge(nodes[0], nodes[2]);
gssw_nodes_add_edge(nodes[1], nodes[3]);
gssw_nodes_add_edge(nodes[2], nodes[3]);
gssw_graph* graph = gssw_graph_create(4);
//memcpy((void*)graph->nodes, (void*)nodes, 4*sizeof(gssw_node*));
//graph->size = 4;
gssw_graph_add_node(graph, nodes[0]);
gssw_graph_add_node(graph, nodes[1]);
gssw_graph_add_node(graph, nodes[2]);
gssw_graph_add_node(graph, nodes[3]);
gssw_graph_fill(graph, read_seq, nt_table, mat, gap_open, gap_extension, 15, 2);
gssw_graph_print_score_matrices(graph, read_seq, strlen(read_seq), stdout);
gssw_graph_mapping* gm = gssw_graph_trace_back (graph,
read_seq,
strlen(read_seq),
match,
mismatch,
gap_open,
gap_extension);
gssw_print_graph_mapping(gm);
gssw_graph_mapping_destroy(gm);
// note that nodes which are referred to in this graph are destroyed as well
gssw_graph_destroy(graph);
free(nt_table);
free(mat);
return(0);
}