/* 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();
}
/* Encodes IDs starting at the given index (id) until "buffer is full"
* or the fastq file ends and writes the result in the given BinaryWriter.
* Updates id according to its advancements.
*/
public void EncodeId(ref int id)
{
// should check if "mode" is right (ie. reader && writer != null)
// but we avoid doing so for efficiency
//the first byte starts with 11 if we are encoding an ID
byte first = (byte)64;
int b = 0;
StringBuilder ids = new StringBuilder();
if (idContinuation.Length != 0)
{
ids.Append(idContinuation);
b += idContinuation.Length;
idContinuation = new StringBuilder();
}
//we assume that a continuation will never be longer
//than BUFFER
while (reader.HasIDLeft(id, 1) && b < ID_BUFFER)
{
string currentId = reader.GetID(id);
b += currentId.Length;
if (b > ID_BUFFER)
{
//continuation
ids.Append(currentId.Substring(0, ID_BUFFER - (b - currentId.Length)));
idContinuation.Append(currentId.Substring(ID_BUFFER - (b - currentId.Length)));
b = ID_BUFFER;
}
else
{
ids.Append(currentId);
}
id++;
//here method to deal with known ID's structure
}
//we use ascii encoding, so 1 char = 1 byte
if (b == ID_BUFFER)
{
writer.Write(first);
writer.Write(ae.GetBytes(ids.ToString()));
}
else if (b < ID_BUFFER)
{
//mark smaller buffer
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(ae.GetBytes(ids.ToString()));
}
}
/* Encodes IDs starting at the given index (id) until "buffer is full"
* or the fastq file ends and writes the result in the given BinaryWriter.
* Updates id according to its advancements.
*/
public void EncodeId(ref int id)
{
idBuffer.Seek(0, SeekOrigin.Begin);
encodedId.Seek(0, SeekOrigin.Begin);
// should check if "mode" is right (ie. reader && writer != null)
// but we avoid doing so for efficiency
//the first byte starts with 11 if we are encoding an ID
byte first = (byte)64;
int b = 0;
if (continuationLength != 0)
{
encodedId.Write(idContinuation, 0, continuationLength);
b += continuationLength;
writtenContinuation = continuationLength;
continuationLength = 0;
}
//we assume that a continuation will never be longer
//than BUFFER
while (reader.HasIDLeft(id, 1) && b < ID_BUFFER)
{
//encodedId.Seek(0, SeekOrigin.Begin);
string[] currentId = reader.GetID(id).Split(separators);
if (currentId.Length < 5)
{
throw new Exception("invalid ID format");
}
//1 2 3 4
//XXX TODO check if you can use only idBuffer and not also encodedID
//the first number that has to be encoded
for (int i = 0; i < 4; i++)
{
encodedId.Write(Convert.ToUInt16(currentId[i + 1]));
// we skip the first item
}
b += ENCODED_ID_LENGTH;
byte[] buffer = ((MemoryStream)encodedId.BaseStream).GetBuffer();
if (b > ID_BUFFER)
{
//continuation
continuationLength = b - ID_BUFFER;
int firstExceedingByte = ENCODED_ID_LENGTH - continuationLength;
for (int i = 0; i < continuationLength; i++)
{
idContinuation[i] = buffer[firstExceedingByte + i];
}
idBuffer.Write(buffer, 0, firstExceedingByte);
//we have to write firstExceedingByte bytes as the count argument
b = ID_BUFFER;
}
else
{
//XXX dopo continuation non scrive primi byte per l'uint?248.1
idBuffer.Write(buffer, 0, ENCODED_ID_LENGTH + writtenContinuation);
}
id++;
encodedId.Seek(0, SeekOrigin.Begin);
writtenContinuation = 0;
}
if (b == ID_BUFFER)
{
writer.Write(first);
writer.Write(((MemoryStream)idBuffer.BaseStream).GetBuffer(), 0, b);
}
else if (b < ID_BUFFER)
{
//mark smaller buffer
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(((MemoryStream)idBuffer.BaseStream).GetBuffer(), 0, b);
}
}
