//splay for one kmer in buffer and save the node to nodeBuffer
static void searchKmer (int t, KmerSet * kset)
{
#ifdef MER127
if( kmerBuffer[t].low2== 0 && N_kmer)
#endif
#ifdef MER63
if( kmerBuffer[t].low== 0 && N_kmer)
#endif
#ifdef MER31
if( kmerBuffer[t]== 0 && N_kmer)
#endif
return ;
kmer_t *node;
boolean found = search_kmerset (kset, kmerBuffer[t], &node);
if (!found)
{
#ifdef MER127
printf ("searchKmer: kmer %llx %llx %llx %llx is not found\n",
kmerBuffer[t].high1, kmerBuffer[t].low1, kmerBuffer[t].high2, kmerBuffer[t].low2);
#endif
#ifdef MER63
printf ("searchKmer: kmer %llx %llx is not found\n",
kmerBuffer[t].high, kmerBuffer[t].low);
#endif
#ifdef MER31
printf ("searchKmer: kmer %llx is not found\n", kmerBuffer[t]);
#endif
}
nodeBuffer[t] = node;
}
static void search1kmerPlus (int j, unsigned char thrdID)
{
kmer_t *node;
boolean found = search_kmerset (KmerSetsPatch[thrdID], mixBuffer[j], &node);
if (!found)
{
mixBuffer[j] =kmerZero;
return;
}
#ifdef MER127
if (smallerBuffer[j])
{
mixBuffer[j].low2 = node->l_links;
}
else
{
mixBuffer[j].low2 = node->l_links + node->twin - 1;
}
#endif
#ifdef MER63
if (smallerBuffer[j])
{
mixBuffer[j].low= node->l_links;
}
else
{
mixBuffer[j].low= node->l_links + node->twin - 1;
}
#endif
#ifdef MER31
if (smallerBuffer[j])
{
mixBuffer[j] = node->l_links;
}
else
{
mixBuffer[j] = node->l_links + node->twin - 1;
}
#endif
}
static void stringBeads ( KMER_PT * firstBead, char nextch, int * node_c )
{
boolean smaller, found;
Kmer tempKmer, bal_word;
Kmer word = firstBead->kmer;
ubyte8 hash_ban;
kmer_t * outgoing_node;
int nodeCounter = 1, setPicker;
char ch;
unsigned char flag;
KMER_PT * temp_pt, *prev_pt = firstBead;
word = prev_pt->kmer;
nodeCounter = 1;
word = nextKmer ( word, nextch );
bal_word = reverseComplement ( word, overlaplen );
if ( KmerLarger ( word, bal_word ) )
{
tempKmer = bal_word;
bal_word = word;
word = tempKmer;
smaller = 0;
}
else
{ smaller = 1; }
hash_ban = hash_kmer ( word );
setPicker = hash_ban % thrd_num;
found = search_kmerset ( KmerSets[setPicker], word, &outgoing_node );
while ( found && ( outgoing_node->linear ) ) // for every node in this line
{
nodeCounter++;
temp_pt = ( KMER_PT * ) stackPush ( nodeStack );
temp_pt->node = outgoing_node;
temp_pt->isSmaller = smaller;
if ( smaller )
{ temp_pt->kmer = word; }
else
{ temp_pt->kmer = bal_word; }
prev_pt = temp_pt;
if ( smaller )
{
for ( ch = 0; ch < 4; ch++ )
{
flag = get_kmer_right_cov ( *outgoing_node, ch );
if ( flag )
{ break; }
}
word = nextKmer ( prev_pt->kmer, ch );
bal_word = reverseComplement ( word, overlaplen );
if ( KmerLarger ( word, bal_word ) )
{
tempKmer = bal_word;
bal_word = word;
word = tempKmer;
smaller = 0;
}
else
{ smaller = 1; }
hash_ban = hash_kmer ( word );
setPicker = hash_ban % thrd_num;
found = search_kmerset ( KmerSets[setPicker], word, &outgoing_node );
}
else
{
for ( ch = 0; ch < 4; ch++ )
{
flag = get_kmer_left_cov ( *outgoing_node, ch );
if ( flag )
{ break; }
}
word = nextKmer ( prev_pt->kmer, int_comp ( ch ) );
bal_word = reverseComplement ( word, overlaplen );
if ( KmerLarger ( word, bal_word ) )
{
tempKmer = bal_word;
bal_word = word;
word = tempKmer;
smaller = 0;
}
else
{ smaller = 1; }
hash_ban = hash_kmer ( word );
setPicker = hash_ban % thrd_num;
found = search_kmerset ( KmerSets[setPicker], word, &outgoing_node );
}
}
if ( outgoing_node ) //this is always true
{
nodeCounter++;
temp_pt = ( KMER_PT * ) stackPush ( nodeStack );
temp_pt->node = outgoing_node;
temp_pt->isSmaller = smaller;
if ( smaller )
{ temp_pt->kmer = word; }
else
{ temp_pt->kmer = bal_word; }
}
*node_c = nodeCounter;
}
