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[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 + 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]);
}
}
}
