void EncodeQual(byte[] buffer, ref long i, BinaryWriter writer, FastqReader reader)
{
//the first byte starts with 0 if we are encoding a quality
byte first = (byte)0;
int b = 0;
if (qualityRunLengthContinuation != 0)
{
buffer[b++] = (byte)qualityRunLengthContinuation;
qualityRunLengthContinuation = 0;
}
while (reader.HasQLeft(i, 1) && b < BUFFER)
{
long j = i + 1;
int rl = 1;
while (reader.HasQLeft(j, 1) && reader.GetQ(j - 1) == reader.GetQ(j) && rl < MAX)
{
j++;
rl++;
}
if (rl > 1) //run length
{
ae.GetBytes(reader.GetQ(j - 1).ToString(), 0, 1, buffer, b);
buffer[b] = (byte)(buffer[b] + 128);
b++;
if (b >= BUFFER)
{
qualityRunLengthContinuation = rl;
}
else
{
buffer[b++] = (byte)rl;
}
i = j;
}
else //single char
{
ae.GetBytes(reader.GetQ(i).ToString(), 0, 1, buffer, b);
b++;
i++;
}
}
if (b == BUFFER)
{
writer.Write(first);
writer.Write(buffer);
}
else
{
first += (byte)32; //we have to tell the decoder that we have a block with a length
//different than BUFFER
writer.Write(first);
writer.Write(b);
writer.Write(buffer, 0, b);
}
}
void EncodeQual(byte[] buffer, ref long i, BinaryWriter writer, FastqReader reader)
{
int b = 0;
if (qualityRunLengthContinuation != 0)
{
buffer[b++] = (byte)qualityRunLengthContinuation;
qualityRunLengthContinuation = 0;
}
while (reader.HasQLeft(i, 1) && b < BUFFER)
{
long j = i + 1;
int rl = 1;
while (reader.HasQLeft(j, 1) && reader.GetQ(j - 1) == reader.GetQ(j) && rl < MAX)
{
j++;
rl++;
}
if (rl > 1) //run length
//ae.GetBytes(reader.GetQ(j-1).ToString(), 0, 1, buffer, b);
{
buffer[b] = Convert.ToByte(reader.GetQ(j - 1));
buffer[b] = (byte)(buffer[b] + 128);
b++;
if (b >= BUFFER)
{
qualityRunLengthContinuation = rl;
}
else
{
buffer[b++] = (byte)rl;
}
i = j;
}
else //single char
//ae.GetBytes(reader.GetQ(i).ToString(), 0, 1, buffer, b);
{
buffer[b] = Convert.ToByte(reader.GetQ(i));
b++;
i++;
}
}
if (b == BUFFER)
{
writer.Write(buffer);
}
else
{
writer.Write(buffer, 0, b);
}
}
//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();
}
/* Main compression method that keeps the two streams aligned and calls
* the encoding methods for sequences and qualities.
*/
public void Compress(FastqReader reader, BinaryWriter writer)
{
long seqI = 0;
long qualI = 0;
int idCounter = 0;
byte[] buffer = new byte[BUFFER];
ChooseIddc(reader, writer);
while (true)
{
Spin("Encoding...");
if (encodeIds && idCounter <= seqI / length && reader.HasIDLeft(idCounter, 1))
{
iddc.EncodeId(ref idCounter);
continue;
}
if ((seqI <= qualI || !encodeQualities) && reader.HasSeqLeft(seqI, 1))
{
EncodeSeq(buffer, ref seqI, writer, reader);
continue;
}
if (encodeQualities && reader.HasQLeft(qualI, 1))
{
EncodeQual(buffer, ref qualI, writer, reader);
continue;
}
break;
}
Console.Error.WriteLine();
}
/* Main compression method that keeps the two streams aligned and calls
* the encoding methods for sequences and qualities.
*/
//public void Compress(FastqReader reader, BinaryWriter writer)
public void Compress(FastqReader reader, BinaryWriter sequenceWriter, BinaryWriter qualityWriter)
{
long seqI = 0;
long qualI = 0;
byte[] buffer = new byte[BUFFER];
while (true)
{
Spin("Encoding...");
if (seqI <= qualI && reader.HasSeqLeft(seqI, 1))
{
EncodeSeq(buffer, ref seqI, sequenceWriter, reader);
continue;
}
if (reader.HasQLeft(qualI, 1))
{
EncodeQual(buffer, ref qualI, qualityWriter, reader);
continue;
}
break;
}
Console.Error.WriteLine();
}
