// WARNING: the kmer atcg is different from soapdenovo's represent
static void output_1edge ( preEDGE2 * long_edge, int K_size, FILE * fp )
{
fprintf ( fp, ">length %d,", long_edge->full_edge->size() - K_size );
const char * seq = long_edge->full_edge->c_str();
//uint64_t from_kmer[2],to_kmer[2];
kmer_t2 from_kmer, to_kmer;
get_kmer_from_seq ( seq, long_edge->full_edge->size() , K_size, 0, &from_kmer );
get_kmer_from_seq ( seq, long_edge->full_edge->size() , K_size, long_edge->full_edge->size() - K_size, &to_kmer );
uint64_t * from, *to;
from = from_kmer.kmer;
to = to_kmer.kmer;
#ifdef _63MER_
fprintf ( fp, "%llx %llx,", from[0], from[1] );
fprintf ( fp, "%llx %llx,", to[0], to[1] );
#endif
#ifdef _127MER_
fprintf ( fp, "%llx %llx %llx %llx,", from[0], from[1], from[2], from[3] );
fprintf ( fp, "%llx %llx %llx %llx,", to[0], to[1], to[2], to[3] );
#endif
fprintf ( fp, "cvg %d,%d\n", long_edge->cvg, long_edge->bal_edge );
fprintf ( fp, "%s", seq );
fprintf ( fp, "\n" );
}
static void chop_kmers ( const char * read, int len, int K_size, kmer_t2 * kmer_array, int kmer_array_len, int & kmer_num )
{
if ( len <= K_size )
{
kmer_num = 0;
return ;
}
kmer_num = len - K_size + 1;
if ( kmer_num > kmer_array_len )
{
fprintf ( stderr, "ERROR: the kmer_array_len is not enough! %d\n", kmer_num );
exit ( 1 );
}
kmer_t2 kmer;
for ( int i = 0; i < kmer_num; ++i ) //optimize later
{
get_kmer_from_seq ( read, len, K_size, i, &kmer );
kmer_array[i] = kmer;
}
}
/*************************************************
Function:
process_edge
Description:
It builds vetexes from one or part of one edge sequence.
Input:
1. v_ht: hashtable
2. K_size: kmer size
3. seq: edge sequence
4. len: edge length
5. type: 1: process head and tail; 2: process head ; 3:process tail
6. edge_id: edge id
7. bal_edge: 0:palindrome 1:else
Output:
None.
Return:
None.
*************************************************/
static void process_edge ( vertex_hash2 * v_ht, int K_size, char * seq, int len, int type, size_t edge_id, bool bal_edge )
{
kmer_t2 vertex_kmer;
kmer_t2 edge_kmer;
vertex2 * v_tmp;
edge_starter2 * e_tmp;
int is_found;
bool is_left;
int edge_kmer_len;
switch ( type )
{
case 1: //process all ..
//process the head
get_kmer_from_seq ( seq, len, K_size, 0, &vertex_kmer );
if ( len <= K_size + gap ) //get the last kmer
{
get_kmer_from_seq ( seq, len, K_size, len - K_size, &edge_kmer );
edge_kmer_len = len - K_size;
}
else
{
//get_kmer_from_seq(seq, len, K_size, K_size,&edge_kmer);
get_kmer_from_seq ( seq, len, K_size, gap, &edge_kmer );
edge_kmer_len = gap;
}
is_left = 0;//right
v_tmp = put_vertex ( v_ht, vertex_kmer, is_found );
put_edge ( v_tmp, edge_kmer, is_left, edge_kmer_len, edge_id );
reverseCompKmer ( &vertex_kmer, K_size );
reverseCompKmer ( &edge_kmer, K_size );
is_left = 1;//left
v_tmp = put_vertex ( v_ht, vertex_kmer, is_found );
put_edge ( v_tmp, edge_kmer, is_left, edge_kmer_len, edge_id + bal_edge );
//process the tail
get_kmer_from_seq ( seq, len, K_size, len - K_size, &vertex_kmer );
if ( len <= K_size + gap ) //get the first kmer
{
get_kmer_from_seq ( seq, len, K_size, 0, &edge_kmer );
edge_kmer_len = len - K_size;
}
else
{
get_kmer_from_seq ( seq, len, K_size, len - K_size - gap, &edge_kmer );
edge_kmer_len = gap;
}
is_left = 1;
v_tmp = put_vertex ( v_ht, vertex_kmer, is_found );
put_edge ( v_tmp, edge_kmer, is_left, edge_kmer_len, edge_id );
reverseCompKmer ( &vertex_kmer, K_size );
reverseCompKmer ( &edge_kmer, K_size );
is_left = 0;//right
v_tmp = put_vertex ( v_ht, vertex_kmer, is_found );
put_edge ( v_tmp, edge_kmer, is_left, edge_kmer_len, edge_id + bal_edge );
break;
case 2:
//process only the head
get_kmer_from_seq ( seq, len, K_size, 0, &vertex_kmer );
if ( len <= K_size + gap )
{
get_kmer_from_seq ( seq, len, K_size, len - K_size, &edge_kmer );
edge_kmer_len = len - K_size;
}
else
{
get_kmer_from_seq ( seq, len, K_size, gap, &edge_kmer );
edge_kmer_len = gap;
}
is_left = 0;//right
v_tmp = put_vertex ( v_ht, vertex_kmer, is_found );
put_edge ( v_tmp, edge_kmer, is_left, edge_kmer_len, edge_id );
reverseCompKmer ( &vertex_kmer, K_size );
reverseCompKmer ( &edge_kmer, K_size );
is_left = 1;//left
v_tmp = put_vertex ( v_ht, vertex_kmer, is_found );
put_edge ( v_tmp, edge_kmer, is_left, edge_kmer_len, edge_id + bal_edge );
break;
case 3:
//process only the tail
get_kmer_from_seq ( seq, len, K_size, len - K_size, &vertex_kmer );
if ( len <= K_size + gap )
{
get_kmer_from_seq ( seq, len, K_size, 0, &edge_kmer );
edge_kmer_len = len - K_size;
}
else
{
get_kmer_from_seq ( seq, len, K_size, len - K_size - gap, &edge_kmer );
edge_kmer_len = gap;
}
is_left = 1;
v_tmp = put_vertex ( v_ht, vertex_kmer, is_found );
put_edge ( v_tmp, edge_kmer, is_left, edge_kmer_len, edge_id );
reverseCompKmer ( &vertex_kmer, K_size );
reverseCompKmer ( &edge_kmer, K_size );
is_left = 0;//right
v_tmp = put_vertex ( v_ht, vertex_kmer, is_found );
put_edge ( v_tmp, edge_kmer, is_left, edge_kmer_len, edge_id + bal_edge );
break;
default:
fprintf ( stderr, "ERROR: wrong process type in process_edge()\n" );
exit ( 1 );
}
}
