//ASCIIEncoding ae = new ASCIIEncoding();
/* Main compression method that keeps the two streams aligned and calls
* the encoding methods for sequences and qualities.
*/
public void Compress(FastqReader reader, BinaryWriter sequenceWriter, BinaryWriter qualityWriter)
{
long seqI = 0;
long qualI = 0;
byte[] buffer = new byte[BUFFER];
WriteBitShepherd bits = new WriteBitShepherd(sequenceWriter);
while (true)
{
Spin("Encoding...");
if (seqI <= qualI && reader.HasSeqLeft(seqI, 1))
{
EncodeSeq(bits, ref seqI, reader);
continue;
}
if (reader.HasQLeft(qualI, 1))
{
EncodeQual(buffer, ref qualI, qualityWriter, reader);
continue;
}
break;
}
bits.Close();
}
/* Encodes sequencing starting at the given index (i) until buffer
* is full or the sequence ends and writes the result in the given WriteBitSheperd.
* Updates i according to its progression.
*/
void EncodeSeq(WriteBitShepherd bits, ref long i, FastqReader reader)
{
int writtenBits = 0;
while (reader.HasSeqLeft(i, 4) && writtenBits < BIT_BUFFER)
{
//Check for run-length run.
if (reader.GetSeq(i) == reader.GetSeq(i + 3) && reader.GetSeq(i) == reader.GetSeq(i + 2) &&
reader.GetSeq(i) == reader.GetSeq(i + 1))
{
long j = i + 4;
long l = i + 8199;
while (j < l && reader.HasSeqLeft(j, 1) && reader.GetSeq(j) == reader.GetSeq(j - 1))
{
j++;
}
int length = (int)(j - i);
if (length > 35)
{
bits.Write(127, 7); //flag for long run length
bits.Write(GetRandomBit(), 1);
bits.Write(Array.IndexOf(Bases, reader.GetSeq(j - 1)), 3);
bits.Write(length - 4, 13);
writtenBits += 24;
}
else
{
bits.Write(0, 7); //flag for short run length
bits.Write(GetRandomBit(), 1);
bits.Write(Array.IndexOf(Bases, reader.GetSeq(j - 1)), 3);
bits.Write(length - 4, 5);
writtenBits += 16;
}
i = j;
}
else
{
bits.Write(Encode(reader.GetSeq(i), reader.GetSeq(i + 1), reader.GetSeq(i + 2)), 7);
bits.Write(GetRandomBit(), 1);
i += 3;
writtenBits += 8;
}
}
bool end = false;
string last = "";
if (!reader.HasSeqLeft(i, 4))
{
while (reader.HasSeqLeft(i, 1)) //could still have 1, 2 or 3 bases
{
last += reader.GetSeq(i++);
}
end = true;
}
if (last != "")
{
last = last.PadRight(3, 'N');
bits.Write(Encode(last[0], last[1], last[2]), 7);
bits.Write(GetRandomBit(), 1);
writtenBits += 8;
}
if (end)
{
bits.Write(126, 7); // mark end of sequences blocks
bits.Write(GetRandomBit(), 1);
writtenBits += 8;
}
}