static void parse1read (int t, int threadID)
{
unsigned int j, retain = 0;
unsigned int edge_index = 0;
kmer_t *node;
boolean isSmaller;
Kmer wordplus, bal_wordplus;
unsigned int start, finish, pos;
Kmer prevKmer, currentKmer;
boolean IsPrevKmer = 0;
start = indexArray[t];
finish = indexArray[t + 1];
pos = start;
for (j = start; j < finish; j++)
{
#ifdef MER127
if( kmerBuffer[j].low2== 0 && N_kmer)
#endif
#ifdef MER63
if( kmerBuffer[j].low== 0 && N_kmer)
#endif
#ifdef MER31
if( kmerBuffer[j]== 0 && N_kmer)
#endif
{
IsPrevKmer=0;
continue;
}
node = nodeBuffer[j];
//extract edges or keep kmers
if ((node->deleted) || (node->linear && !node->inEdge)) // deleted or in a floating loop
{
if (retain < 2)
{
retain = 0;
pos = start;
}
else
{
break;
}
continue;
}
isSmaller = smallerBuffer[j];
if (node->linear)
{
if (isSmaller)
{
edge_index = node->l_links;
}
else
{
edge_index = node->l_links + node->twin - 1;
}
#ifdef MER127
if (retain == 0 || IsPrevKmer)
{
retain++;
mixBuffer[pos].low2 = edge_index;
flagArray[pos++] = 0;
IsPrevKmer = 0;
}
else if (edge_index != mixBuffer[pos - 1].low2)
{
retain++;
mixBuffer[pos].low2 = edge_index;
flagArray[pos++] = 0;
}
#endif
#ifdef MER63
if (retain == 0 || IsPrevKmer)
{
retain++;
mixBuffer[pos].low= edge_index;
flagArray[pos++] = 0;
IsPrevKmer = 0;
}
else if (edge_index != mixBuffer[pos - 1].low)
{
retain++;
mixBuffer[pos].low= edge_index;
flagArray[pos++] = 0;
}
#endif
#ifdef MER31
if (retain == 0 || IsPrevKmer)
{
retain++;
mixBuffer[pos] = edge_index;
flagArray[pos++] = 0;
IsPrevKmer = 0;
}
else if (edge_index != mixBuffer[pos - 1])
{
retain++;
mixBuffer[pos] = edge_index;
flagArray[pos++] = 0;
}
#endif
}
else
{
if (isSmaller)
{
currentKmer = node->seq;
}
else
{
currentKmer = reverseComplement (node->seq, overlaplen);
}
if (IsPrevKmer)
{
retain++;
wordplus = KmerPlus (prevKmer, lastCharInKmer (currentKmer));
bal_wordplus = reverseComplement (wordplus, overlaplen + 1);
if (KmerSmaller (wordplus, bal_wordplus))
{
smallerBuffer[pos] = 1;
hashBanBuffer[pos] = hash_kmer (wordplus);
mixBuffer[pos] = wordplus;
}
else
{
smallerBuffer[pos] = 0;
hashBanBuffer[pos] = hash_kmer (bal_wordplus);
mixBuffer[pos] = bal_wordplus;
}
// fprintf(stderr,"%lld\n",hashBanBuffer[pos]);
flagArray[pos++] = 1;
}
IsPrevKmer = 1;
prevKmer = currentKmer;
}
}
/*
for(j=start;j<pos;j++)
fprintf(stderr,"%d ",flagArray[j]);
fprintf(stderr,"\n");
*/
if (retain < 1)
{
deletion[threadID]++;
}
if (retain < 2)
{
flagArray[start] = 0;
mixBuffer[start] = kmerZero;
return;
}
if ((pos - start) != retain)
{
printf ("read %d, %d vs %d\n", t, retain, edge_index - start);
}
if (pos < finish)
{
flagArray[pos] = 0;
mixBuffer[pos] = kmerZero;
}
}
static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, FILE * fp )
{
int length, char_index;
preEDGE * newedge;
kmer_t * del_node, *longNode;
char * tightSeq, firstCh;
long long symbol = 0;
int len_tSeq;
Kmer wordplus, bal_wordplus;
ubyte8 hash_ban;
KMER_PT * last_np = ( KMER_PT * ) stackPop ( nStack );
KMER_PT * second_last_np = ( KMER_PT * ) stackPop ( nStack );
KMER_PT * first_np, *second_np = NULL;
KMER_PT * temp;
boolean found, lastOne = 1, single = 1;
int setPicker;
length = count - 1;
len_tSeq = length;
if ( len_tSeq >= edge_length_limit )
{ tightSeq = ( char * ) ckalloc ( len_tSeq * sizeof ( char ) ); }
else
{ tightSeq = edge_seq; }
char_index = length - 1;
newedge = &temp_edge;
newedge->to_node = last_np->kmer;
newedge->length = length;
newedge->bal_edge = bal_edge;
tightSeq[char_index--] = lastCharInKmer ( last_np->kmer );
firstCh = firstCharInKmer ( second_last_np->kmer );
dislink2prevUncertain ( last_np->node, firstCh, last_np->isSmaller );
stackRecover ( nStack );
while ( nStack->item_c > 1 )
{
second_np = ( KMER_PT * ) stackPop ( nStack );
}
first_np = ( KMER_PT * ) stackPop ( nStack );
//unlink first node to the second one
dislink2nextUncertain ( first_np->node, lastCharInKmer ( second_np->kmer ), first_np->isSmaller );
//printf("from %llx, to %llx\n",first_np->node->seq,last_np->node->seq);
//now temp is the last node in line, out_node is the second last node in line
newedge->from_node = first_np->kmer;
//create a long kmer for edge with length 1
if ( length == 1 )
{
nodeCounter++;
wordplus = KmerPlus ( newedge->from_node, lastCharInKmer ( newedge->to_node ) );
bal_wordplus = reverseComplement ( wordplus, overlaplen + 1 );
/*
Kmer temp = KmerPlus(reverseComplement(newedge->to_node,overlaplen),
lastCharInKmer(reverseComplement(newedge->from_node,overlaplen)));
fprintf(stderr,"(%llx %llx) (%llx %llx) (%llx %llx)\n",
wordplus.high,wordplus.low,temp.high,temp.low,
bal_wordplus.high,bal_wordplus.low);
*/
edge_c++;
edgeCounter++;
if ( KmerSmaller ( wordplus, bal_wordplus ) )
{
hash_ban = hash_kmer ( wordplus );
setPicker = hash_ban % thrd_num;
found = put_kmerset ( KmerSetsPatch[setPicker], wordplus, 4, 4, &longNode );
if ( found )
{ printf ( "longNode %llx %llx already exist\n", wordplus.high, wordplus.low ); }
longNode->l_links = edge_c;
longNode->twin = ( unsigned char ) ( bal_edge + 1 );
}
else
{
hash_ban = hash_kmer ( bal_wordplus );
setPicker = hash_ban % thrd_num;
found = put_kmerset ( KmerSetsPatch[setPicker], bal_wordplus, 4, 4, &longNode );
if ( found )
{ printf ( "longNode %llx %llx already exist\n", bal_wordplus.high, bal_wordplus.low ); }
longNode->l_links = edge_c + bal_edge;
longNode->twin = ( unsigned char ) ( -bal_edge + 1 );
}
}
else
{
edge_c++;
edgeCounter++;
}
stackRecover ( nStack );
//mark all the internal nodes
temp = ( KMER_PT * ) stackPop ( nStack );
while ( nStack->item_c > 1 )
{
temp = ( KMER_PT * ) stackPop ( nStack );
del_node = temp->node;
del_node->inEdge = 1;
symbol += get_kmer_left_covs ( *del_node );
if ( temp->isSmaller )
{
del_node->l_links = edge_c;
del_node->twin = ( unsigned char ) ( bal_edge + 1 );
}
else
{
del_node->l_links = edge_c + bal_edge;
del_node->twin = ( unsigned char ) ( -bal_edge + 1 );
}
tightSeq[char_index--] = lastCharInKmer ( temp->kmer );
}
newedge->seq = tightSeq;
if ( length > 1 )
{ newedge->cvg = symbol / ( length - 1 ) * 10 > MaxEdgeCov ? MaxEdgeCov : symbol / ( length - 1 ) * 10; }
else
{ newedge->cvg = 0; }
output_1edge ( newedge, fp );
if ( len_tSeq >= edge_length_limit )
{ free ( ( void * ) tightSeq ); }
edge_c += bal_edge;
if ( edge_c % 10000000 == 0 )
{ printf ( "--- %d edges built\n", edge_c ); }
return;
}