public int[] SeqParse(int rowIndex)
{
string seq = FetchSeq(rowIndex);
int[] freq = new int[reg.Length];
Multithreading.StartLoops(0, reg.Length,
i => { freq[i] = reg[i].Matches(seq).Count; });
return(freq);
}
public int[] SeqParse2(uint seqIdx, uint seqLen)
{
string seq = FetchSeq(seqIdx, seqLen);
int[] freq = new int[reg.Length];
if (seq == null)
{
return(freq);
}
Multithreading.StartLoops(0, reg.Length,
i => { freq[i] = reg[i].Matches(seq).Count; });
return(freq);
}
public uint[] KmerFrequency(byte[] seq, int k)
{
uint N = (uint)(1 << (2 * k));
uint mask = (uint)(N - 1);
uint[] freq = new uint[N];
uint[] freq2 = new uint[freq.Length];
uint[] tmp;
uint idx = 0;
uint kLen = 0;
for (uint i = 0; i < seq.Length; i++)
{
byte nb = seq[i];
if (nb == 4) // unknown nucliotide
{
kLen = idx = 0;
continue;
}
idx = ((idx << 2) & mask) | (uint)(nb & 3);
kLen++;
if (kLen >= k)
{
freq[idx]++;
}
}
Multithreading.StartLoops(0, (int)N, delegate(int n) {
// Flip the index n to n3.
uint n2 = ((uint)n) ^ 0xFFFFFFFF; // A->T, G->C
uint n3 = 0; // Reverse the bi-bits order
for (int i = 0; i < k; i++)
{
n3 <<= 2;
n3 |= (n2 & 0x3);
n2 >>= 2;
}
freq2[n] = freq[n] + freq[n3];
});
tmp = freq2; freq2 = freq; freq = tmp;
if (!allowMismatch)
{
return(freq);
}
// including the single nb mutation.
Multithreading.StartLoops(0, (int)N, delegate(int n) {
uint sum = freq[n];
for (int i = 0; i < 2 * k; i += 2)
{
sum += freq[n ^ (1 << i)] + freq2[n ^ (2 << i)] + freq2[n ^ (3 << i)];
}
freq2[n] = sum;
});
// including the single nb deletions.
tmp = freq2; freq2 = freq; freq = tmp;
Multithreading.StartLoops(0, (int)N, delegate(int n) {
uint sum = freq[n];
for (int i = 0; i < k; i++)
{
for (int nb = 0; nb < 4; nb++)
{
for (int leftFlank = 0; leftFlank < 2; leftFlank++)
{
int i2 = 2 * i;
int m = 0;
int rMask = (1 << i2) - 1; // mask for the section on the right side of the deleted nb.
if (leftFlank == 1)
{
// the (k-1) will be extend to k-mer by add nb to the left side.
int rightSec = n & rMask;
int leftSec = (n >> 2) & ~rMask;
m = (nb << (2 * k - 2)) | leftSec | rightSec;
}
else
{
// the (k-1) will be extend to k-mer by add nb to the right side.
int rightSec = (n & rMask) << 2;
int leftSec = ((n >> (i2 + 2)) << (i2 + 2));
m = leftSec | rightSec | nb;
}
sum += freq[m];
}
}
}
freq2[n] = sum;
});
return(freq2);
}