static void chopKmer4read ( int t, int threadID )
{
char * src_seq = seqBuffer[t];
char * bal_seq = rcSeq[threadID];
int len_seq = lenBuffer[t];
int j, bal_j;
ubyte8 hash_ban, bal_hash_ban;
Kmer word, bal_word;
int index;
char InvalidCh = 4;
#ifdef MER127
word.high1 = word.low1 = word.high2 = word.low2 = 0;
for ( index = 0; index < overlaplen; index++ )
{
word = KmerLeftBitMoveBy2 ( word );
word.low2 |= src_seq[index];
}
#else
word.high = word.low = 0;
for ( index = 0; index < overlaplen; index++ )
{
word = KmerLeftBitMoveBy2 ( word );
word.low |= src_seq[index];
}
#endif
reverseComplementSeq ( src_seq, len_seq, bal_seq );
// complementary node
bal_word = reverseComplement ( word, overlaplen );
bal_j = len_seq - overlaplen;
index = indexArray[t];
if ( KmerSmaller ( word, bal_word ) )
{
hash_ban = hash_kmer ( word );
hashBanBuffer[index] = hash_ban;
kmerBuffer[index] = word;
prevcBuffer[index] = InvalidCh;
nextcBuffer[index++] = src_seq[0 + overlaplen];
}
else
{
bal_hash_ban = hash_kmer ( bal_word );
hashBanBuffer[index] = bal_hash_ban;
kmerBuffer[index] = bal_word;
prevcBuffer[index] = bal_seq[bal_j - 1];
nextcBuffer[index++] = InvalidCh;
}
for ( j = 1; j <= len_seq - overlaplen; j++ )
{
word = nextKmer ( word, src_seq[j - 1 + overlaplen] );
bal_j = len_seq - j - overlaplen;
bal_word = prevKmer ( bal_word, bal_seq[bal_j] );
if ( KmerSmaller ( word, bal_word ) )
{
hash_ban = hash_kmer ( word );
hashBanBuffer[index] = hash_ban;
kmerBuffer[index] = word;
prevcBuffer[index] = src_seq[j - 1];
if ( j < len_seq - overlaplen )
{
nextcBuffer[index++] = src_seq[j + overlaplen];
}
else
{
nextcBuffer[index++] = InvalidCh;
}
//printf("%dth: %p with %p\n",kmer_c-1,word,hashBanBuffer[kmer_c-1]);
}
else
{
// complementary node
bal_hash_ban = hash_kmer ( bal_word );
hashBanBuffer[index] = bal_hash_ban;
kmerBuffer[index] = bal_word;
if ( bal_j > 0 )
{
prevcBuffer[index] = bal_seq[bal_j - 1];
}
else
{
prevcBuffer[index] = InvalidCh;
}
nextcBuffer[index++] = bal_seq[bal_j + overlaplen];
//printf("%dth: %p with %p\n",kmer_c-1,bal_word,hashBanBuffer[kmer_c-1]);
}
}
}
static void chopKmer4read (int t, int threadID)
{
char *src_seq = seqBuffer[t];
char *bal_seq = rcSeq[threadID];
int len_seq = lenBuffer[t];
int j, bal_j;
ubyte8 hash_ban, bal_hash_ban;
Kmer word, bal_word;
int index;
//mao 2011 10 8
Kmer InvalidKmer ;
InvalidKmer=kmerZero;
int n_num;
word = kmerZero;
for (index = 0; index < overlaplen; index++)
{
#ifdef MER127
word = KmerLeftBitMoveBy2(word);
word.low2 |= src_seq[index];
#endif
#ifdef MER63
word = KmerLeftBitMoveBy2(word);
word.low |= src_seq[index];
#endif
#ifdef MER31
word = KmerLeftBitMoveBy2(word);
word += src_seq[index];
#endif
//mao 2011 10 8
if(src_seq[index] == 4)
n_num = overlaplen;
else if(n_num >0)
n_num--;
}
reverseComplementSeq (src_seq, len_seq, bal_seq);
// complementary node
bal_word = reverseComplement (word, overlaplen);
bal_j = len_seq - 0 - overlaplen; // 0;
index = indexArray[t];
//mao 2011 10 8
if(n_num > 0 && N_kmer)
{
hash_ban = hash_kmer (InvalidKmer);
hashBanBuffer[index] = hash_ban;
kmerBuffer[index] = InvalidKmer;
smallerBuffer[index] = 1;
}
else if (KmerSmaller (word, bal_word))
{
hash_ban = hash_kmer (word);
kmerBuffer[index] = word;
smallerBuffer[index] = 1;
hashBanBuffer[index++] = hash_ban;
}
else
{
bal_hash_ban = hash_kmer (bal_word);
kmerBuffer[index] = bal_word;
smallerBuffer[index] = 0;
hashBanBuffer[index++] = bal_hash_ban;
}
//printf("%dth: %p with %p\n",kmer_c-1,bal_word,bal_hash_ban);
for (j = 1; j <= len_seq - overlaplen; j++)
{
word = nextKmer (word, src_seq[j - 1 + overlaplen]);
bal_j = len_seq - j - overlaplen; // j;
bal_word = reverseComplement (word, overlaplen);
//mao 2011 10 8
if(src_seq[j - 1 + overlaplen] == 4)
n_num = overlaplen;
else if(n_num >0)
n_num--;
//mao 2011 10 8
if(n_num > 0 && N_kmer)
{
hash_ban = hash_kmer (InvalidKmer);
hashBanBuffer[index] = hash_ban;
kmerBuffer[index] = InvalidKmer;
smallerBuffer[index] = 1;
}
else if (KmerSmaller (word, bal_word))
{
hash_ban = hash_kmer (word);
kmerBuffer[index] = word;
smallerBuffer[index] = 1;
hashBanBuffer[index++] = hash_ban;
//printf("%dth: %p with %p\n",kmer_c-1,word,hashBanBuffer[kmer_c-1]);
}
else
{
// complementary node
bal_hash_ban = hash_kmer (bal_word);
kmerBuffer[index] = bal_word;
smallerBuffer[index] = 0;
hashBanBuffer[index++] = bal_hash_ban;
//printf("%dth: %p with %p\n",kmer_c-1,bal_word,hashBanBuffer[kmer_c-1]);
}
}
}
static void chopKmer4read (int t, int threadID)
{
char *src_seq = seqBuffer + seqBreakers[t];
char *bal_seq = rcSeq[threadID];
int len_seq = lenBuffer[t];
int j, bal_j;
ubyte8 hash_ban, bal_hash_ban;
Kmer word, bal_word;
int index;
word=kmerZero;
for (index = 0; index < overlaplen; index++)
{
word = KmerLeftBitMoveBy2 (word);
#ifdef MER127
word.low2 |= src_seq[index];
#endif
#ifdef MER63
word.low|= src_seq[index];
#endif
#ifdef MER31
word |= src_seq[index];
#endif
}
reverseComplementSeq (src_seq, len_seq, bal_seq);
// complementary node
bal_word = reverseComplement (word, overlaplen);
bal_j = len_seq - 0 - overlaplen; // 0;
index = indexArray[t];
if (KmerSmaller (word, bal_word))
{
hash_ban = hash_kmer (word);
kmerBuffer[index] = word;
hashBanBuffer[index] = hash_ban;
smallerBuffer[index++] = 1;
}
else
{
bal_hash_ban = hash_kmer (bal_word);
kmerBuffer[index] = bal_word;
hashBanBuffer[index] = bal_hash_ban;
smallerBuffer[index++] = 0;
}
//printf("%dth: %p with %p\n",kmer_c-1,bal_word,bal_hash_ban);
for (j = 1; j <= len_seq - overlaplen; j++)
{
word = nextKmer (word, src_seq[j - 1 + overlaplen]);
bal_j = len_seq - j - overlaplen; // j;
bal_word = prevKmer (bal_word, bal_seq[bal_j]);
if (KmerSmaller (word, bal_word))
{
hash_ban = hash_kmer (word);
kmerBuffer[index] = word;
hashBanBuffer[index] = hash_ban;
smallerBuffer[index++] = 1;
//printf("%dth: %p with %p\n",kmer_c-1,word,hashBanBuffer[kmer_c-1]);
}
else
{
// complementary node
bal_hash_ban = hash_kmer (bal_word);
kmerBuffer[index] = bal_word;
hashBanBuffer[index] = bal_hash_ban;
smallerBuffer[index++] = 0;
//printf("%dth: %p with %p\n",kmer_c-1,bal_word,hashBanBuffer[kmer_c-1]);
}
}
}
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;
}
static void chopKmer4read(int t, int threadID)
{
char *src_seq = seqBuffer + seqBreakers[t];
char *bal_seq = rcSeq[threadID];
int len_seq = lenBuffer[t];
int j, bal_j;
Kmer hash_ban, bal_hash_ban;
Kmer word, bal_word;
int index;
word = 0;
for (index = 0; index < overlaplen; index++)
{
word <<= 2;
word += src_seq[index];
}
reverseComplementSeq(src_seq, len_seq, bal_seq);
// complementary node
bal_word = reverseComplement(word, overlaplen);
bal_j = len_seq - 0 - overlaplen; // 0;
index = indexArray[t];
if(word < bal_word)
{
hash_ban = hash_kmer(word);
kmerBuffer[index] = word;
hashBanBuffer[index] = hash_ban;
smallerBuffer[index++] = 1;
}
else
{
bal_hash_ban = hash_kmer(bal_word);
kmerBuffer[index] = bal_word;
hashBanBuffer[index] = bal_hash_ban;
smallerBuffer[index++] = 0;
}
//printf("%dth: %p with %p\n",kmer_c-1,bal_word,bal_hash_ban);
for(j = 1; j <= len_seq - overlaplen; j ++)
{
word = nextKmer(word, src_seq[j - 1 + overlaplen]);
bal_j = len_seq - j - overlaplen; // j;
bal_word = prevKmer(bal_word, bal_seq[bal_j]);
if(word < bal_word)
{
hash_ban = hash_kmer(word);
kmerBuffer[index] = word;
hashBanBuffer[index] = hash_ban;
smallerBuffer[index++] = 1;
//printf("%dth: %p with %p\n",kmer_c-1,word,hashBanBuffer[kmer_c-1]);
}
else
{
// complementary node
bal_hash_ban = hash_kmer(bal_word);
kmerBuffer[index] = bal_word;
hashBanBuffer[index] = bal_hash_ban;
smallerBuffer[index++] = 0;
//printf("%dth: %p with %p\n",kmer_c-1,bal_word,hashBanBuffer[kmer_c-1]);
}
}
}