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);
}
}