/// <summary>
/// Parses the sequences out of a stream.
/// </summary>
/// <param name="stream">Stream to read from</param>
/// <returns>Set of sequences</returns>
public IEnumerable <ISequence> Parse(Stream stream)
{
using (BinaryReader reader = new BinaryReader(stream, Encoding.ASCII))
{
parsedHeader = ParseHeader(reader);
for (lastIndex = 0; lastIndex < parsedHeader.NumberOfReads; lastIndex++)
{
yield return(ParseOne(parsedHeader, reader));
}
}
parsedHeader = null;
lastIndex = 0;
}
/// <summary>
/// Parse a sequence out of a stream.
/// </summary>
/// <param name="stream">Stream to read from</param>
/// <returns>Sequence</returns>
public ISequence ParseOne(Stream stream)
{
using (BinaryReader reader = new BinaryReader(stream, Encoding.ASCII))
{
if (parsedHeader == null)
{
parsedHeader = ParseHeader(reader);
lastIndex = 0;
}
if (parsedHeader.NumberOfReads > lastIndex)
{
lastIndex++;
return(ParseOne(parsedHeader, reader));
}
}
parsedHeader = null;
lastIndex = 0;
return(null);
}
/// <summary>
/// Parse a sequence out of a stream.
/// </summary>
/// <param name="stream">Stream to read from</param>
/// <returns>Sequence</returns>
public ISequence ParseOne(Stream stream)
{
using (BinaryReader reader = new BinaryReader(stream, AsciiEncoding.Default))
{
if (parsedHeader == null)
{
parsedHeader = ParseHeader(reader);
lastIndex = 0;
}
if (parsedHeader.NumberOfReads > lastIndex)
{
lastIndex++;
return ParseOne(parsedHeader, reader);
}
}
parsedHeader = null;
lastIndex = 0;
return null;
}
/// <summary>
/// Parses out the header from the file
/// </summary>
/// <param name="reader"></param>
/// <returns></returns>
private SffHeader ParseHeader(BinaryReader reader)
{
// Fixed header block
// magic_number uint32 +4 = 0-3
// version char[4] +4 = 4-7
// index_offset uint64 +8 = 8-15
// index_length uint32 +4 = 16-19
// number_of_reads uint32 +4 = 20-23
// header_length uint16 +2 = 24-25
// key_length uint16 +2 = 26-27
// number_of_flows_per_read uint16 +2 = 28-29
// flowgram_format_code uint8 +1 = 30
const uint magicNumber = 0x2e736666; // ".sff"
const int fixedHeaderSize = 31;
// First, parse out the header to verify the file format.
// Check the magic string
if (C2BE(reader.ReadUInt32()) != magicNumber)
{
throw new Exception("Missing .sff magic number - cannot parse.");
}
// Parse out all the fixed header elements.
var header = new SffHeader
{
Version = C2BE(reader.ReadUInt32()),
IndexOffset = C2BE(reader.ReadUInt64()),
IndexLength = C2BE(reader.ReadUInt32()),
NumberOfReads = C2BE(reader.ReadUInt32()),
Length = C2BE(reader.ReadUInt16()),
KeyLength = C2BE(reader.ReadUInt16()),
NumberOfFlowsPerRead = C2BE(reader.ReadUInt16()),
FlowgramFormatCode = reader.ReadByte()
};
if (header.Version != 1)
{
throw new Exception("Unexpected SFF version number (" + header.Version + "), can only parse V1");
}
if (header.FlowgramFormatCode != 1)
{
throw new Exception("Unexpected SFF flowgram format (" + header.FlowgramFormatCode +
"), only recognize format 1.");
}
// Grab the flow characters
header.FlowChars = new char[header.NumberOfFlowsPerRead];
int readBytes = reader.Read(header.FlowChars, 0, header.NumberOfFlowsPerRead);
if (readBytes != header.NumberOfFlowsPerRead)
{
throw new Exception("Could not parse header (flow_chars).");
}
char[] keySequence = new char[header.KeyLength];
readBytes = reader.Read(keySequence, 0, header.KeyLength);
if (readBytes != header.KeyLength)
{
throw new Exception("Could not parse header (key_sequence).");
}
header.KeySequence = new string(keySequence);
// Calculate the padding
int paddingSize = header.Length - (fixedHeaderSize + header.NumberOfFlowsPerRead + header.KeyLength);
if (paddingSize < 0 || paddingSize > 8)
{
throw new Exception("Invalid header size found.");
}
if (paddingSize > 0)
{
if (reader.Read(new char[8], 0, paddingSize) != paddingSize)
{
throw new Exception("Could not parse header (padding).");
}
}
return(header);
}
/// <summary>
/// Parses a single sequence from the file.
/// </summary>
/// <param name="header">Parsed header</param>
/// <param name="reader">Binary reader</param>
/// <returns>Sequence</returns>
private ISequence ParseOne(SffHeader header, BinaryReader reader)
{
// Parse out the read header.
ushort headerLength = C2BE(reader.ReadUInt16());
ushort nameLength = C2BE(reader.ReadUInt16());
uint numberOfBases = C2BE(reader.ReadUInt32());
// TODO: use clipping data
ushort clipQualityLeft = C2BE(reader.ReadUInt16());
ushort clipQualityRight = C2BE(reader.ReadUInt16());
ushort clipAdapterLeft = C2BE(reader.ReadUInt16());
ushort clipAdapterRight = C2BE(reader.ReadUInt16());
string name = new string(reader.ReadChars(nameLength));
long paddingSize = headerLength - (16 + nameLength);
if (paddingSize < 0 || paddingSize > 8)
{
throw new Exception("Invalid read header size found.");
}
if (paddingSize > 0)
{
if (reader.Read(new char[8], 0, (int)paddingSize) != paddingSize)
{
throw new Exception("Could not parse read header (padding).");
}
}
// Parse out the read data section
ushort[] flowgramValues = new ushort[header.NumberOfFlowsPerRead];
for (int flowCount = 0; flowCount < header.NumberOfFlowsPerRead; flowCount++)
{
flowgramValues[flowCount] = C2BE(reader.ReadUInt16());
}
byte[] flowIndexPerBase = new byte[numberOfBases];
if (reader.Read(flowIndexPerBase, 0, (int)numberOfBases) != numberOfBases)
{
throw new Exception("Unable to read flow indexes.");
}
byte[] bases = new byte[numberOfBases];
if (reader.Read(bases, 0, (int)numberOfBases) != numberOfBases)
{
throw new Exception("Unable to read base information.");
}
byte[] qscores = new byte[numberOfBases];
if (reader.Read(qscores, 0, (int)numberOfBases) != numberOfBases)
{
throw new Exception("Unable to read quality scores.");
}
for (int i = 0; i < qscores.Length; i++)
{
qscores[i] += 33; // adjust for Sanger
}
// Adjust for 8-byte padding at end of read segment
long currentSize = header.NumberOfFlowsPerRead * 2 + 3 * numberOfBases;
if ((currentSize & 7) > 0)
{
paddingSize = (((currentSize >> 3) + 1) << 3) - currentSize;
if (paddingSize < 0 || paddingSize > 8)
{
throw new Exception("Invalid read data size found.");
}
if (paddingSize > 0)
{
if (reader.Read(new char[8], 0, (int)paddingSize) != paddingSize)
{
throw new Exception("Could not parse read header (padding).");
}
}
}
// Determine the alphabet.
var alphabet = Alphabet
?? Alphabets.AutoDetectAlphabet(bases, 0, bases.Length, null)
?? Alphabets.AmbiguousDNA;
// Return our qSequence
return(new QualitativeSequence(alphabet, FastQFormatType.Sanger, bases, qscores, false)
{
ID = name
});
}
/// <summary>
/// Parses out the header from the file
/// </summary>
/// <param name="reader"></param>
/// <returns></returns>
private SffHeader ParseHeader(BinaryReader reader)
{
// Fixed header block
// magic_number uint32 +4 = 0-3
// version char[4] +4 = 4-7
// index_offset uint64 +8 = 8-15
// index_length uint32 +4 = 16-19
// number_of_reads uint32 +4 = 20-23
// header_length uint16 +2 = 24-25
// key_length uint16 +2 = 26-27
// number_of_flows_per_read uint16 +2 = 28-29
// flowgram_format_code uint8 +1 = 30
const uint magicNumber = 0x2e736666; // ".sff"
const int fixedHeaderSize = 31;
// First, parse out the header to verify the file format.
// Check the magic string
if (C2BE(reader.ReadUInt32()) != magicNumber)
throw new Exception("Missing .sff magic number - cannot parse.");
// Parse out all the fixed header elements.
var header = new SffHeader
{
Version = C2BE(reader.ReadUInt32()),
IndexOffset = C2BE(reader.ReadUInt64()),
IndexLength = C2BE(reader.ReadUInt32()),
NumberOfReads = C2BE(reader.ReadUInt32()),
Length = C2BE(reader.ReadUInt16()),
KeyLength = C2BE(reader.ReadUInt16()),
NumberOfFlowsPerRead = C2BE(reader.ReadUInt16()),
FlowgramFormatCode = reader.ReadByte()
};
if (header.Version != 1)
throw new Exception("Unexpected SFF version number (" + header.Version + "), can only parse V1");
if (header.FlowgramFormatCode != 1)
throw new Exception("Unexpected SFF flowgram format (" + header.FlowgramFormatCode +
"), only recognize format 1.");
// Grab the flow characters
header.FlowChars = new char[header.NumberOfFlowsPerRead];
int readBytes = reader.Read(header.FlowChars, 0, header.NumberOfFlowsPerRead);
if (readBytes != header.NumberOfFlowsPerRead)
throw new Exception("Could not parse header (flow_chars).");
char[] keySequence = new char[header.KeyLength];
readBytes = reader.Read(keySequence, 0, header.KeyLength);
if (readBytes != header.KeyLength)
throw new Exception("Could not parse header (key_sequence).");
header.KeySequence = new string(keySequence);
// Calculate the padding
int paddingSize = header.Length - (fixedHeaderSize + header.NumberOfFlowsPerRead + header.KeyLength);
if (paddingSize < 0 || paddingSize > 8)
throw new Exception("Invalid header size found.");
if (paddingSize > 0)
{
if (reader.Read(new char[8], 0, paddingSize) != paddingSize)
throw new Exception("Could not parse header (padding).");
}
return header;
}
/// <summary>
/// Parses a single sequence from the file.
/// </summary>
/// <param name="header">Parsed header</param>
/// <param name="reader">Binary reader</param>
/// <returns>Sequence</returns>
private ISequence ParseOne(SffHeader header, BinaryReader reader)
{
// Parse out the read header.
ushort headerLength = C2BE(reader.ReadUInt16());
ushort nameLength = C2BE(reader.ReadUInt16());
uint numberOfBases = C2BE(reader.ReadUInt32());
// TODO: use clipping data
ushort clipQualityLeft = C2BE(reader.ReadUInt16());
ushort clipQualityRight = C2BE(reader.ReadUInt16());
ushort clipAdapterLeft = C2BE(reader.ReadUInt16());
ushort clipAdapterRight = C2BE(reader.ReadUInt16());
string name = new string(reader.ReadChars(nameLength));
long paddingSize = headerLength - (16 + nameLength);
if (paddingSize < 0 || paddingSize > 8)
throw new Exception("Invalid read header size found.");
if (paddingSize > 0)
{
if (reader.Read(new char[8], 0, (int)paddingSize) != paddingSize)
throw new Exception("Could not parse read header (padding).");
}
// Parse out the read data section
ushort[] flowgramValues = new ushort[header.NumberOfFlowsPerRead];
for (int flowCount = 0; flowCount < header.NumberOfFlowsPerRead; flowCount++)
flowgramValues[flowCount] = C2BE(reader.ReadUInt16());
byte[] flowIndexPerBase = new byte[numberOfBases];
if (reader.Read(flowIndexPerBase, 0, (int)numberOfBases) != numberOfBases)
throw new Exception("Unable to read flow indexes.");
byte[] bases = new byte[numberOfBases];
if (reader.Read(bases, 0, (int)numberOfBases) != numberOfBases)
throw new Exception("Unable to read base information.");
byte[] qscores = new byte[numberOfBases];
if (reader.Read(qscores, 0, (int)numberOfBases) != numberOfBases)
throw new Exception("Unable to read quality scores.");
for (int i = 0; i < qscores.Length; i++)
qscores[i] += 33; // adjust for Sanger
// Adjust for 8-byte padding at end of read segment
long currentSize = header.NumberOfFlowsPerRead*2 + 3*numberOfBases;
if ((currentSize & 7) > 0)
{
paddingSize = (((currentSize >> 3) + 1) << 3) - currentSize;
if (paddingSize < 0 || paddingSize > 8)
throw new Exception("Invalid read data size found.");
if (paddingSize > 0)
{
if (reader.Read(new char[8], 0, (int)paddingSize) != paddingSize)
throw new Exception("Could not parse read header (padding).");
}
}
// Determine the alphabet.
var alphabet = Alphabet
?? Alphabets.AutoDetectAlphabet(bases, 0, bases.Length, null)
?? Alphabets.AmbiguousDNA;
// Return our qSequence
return new QualitativeSequence(alphabet, FastQFormatType.Sanger, bases, qscores, false) { ID = name };
}
/// <summary>
/// Parses the sequences out of a stream.
/// </summary>
/// <param name="stream">Stream to read from</param>
/// <returns>Set of sequences</returns>
public IEnumerable<ISequence> Parse(Stream stream)
{
using (BinaryReader reader = new BinaryReader(stream, AsciiEncoding.Default))
{
parsedHeader = ParseHeader(reader);
for (lastIndex = 0; lastIndex < parsedHeader.NumberOfReads; lastIndex++)
{
yield return ParseOne(parsedHeader, reader);
}
}
parsedHeader = null;
lastIndex = 0;
}
