void ChooseIddc(EncodedFastqReader reader)
{
if (!encodeIds)
{
iddc = new PlaceholderIdGenerator();
return;
}
int iddcType = reader.Reader.ReadInt32();
if (iddcType == 0)
{
iddc = new SraIdDeCompresser(reader, length);
}
else if (iddcType == 1)
{
iddc = new PlainIdDeCompresser(reader);
}
else if (iddcType == 2)
{
iddc = new EncodeIdDeCompresser(reader);
}
else
{
throw new Exception("Missing header info in compressed file! " + iddcType);
}
}
public SraIdDeCompresser(EncodedFastqReader encReader, int length)
{
this.encReader = encReader;
int l = encReader.Reader.ReadInt32();
string firstIdPart = ae.GetString(encReader.Reader.ReadBytes(l)); //@SRX000571_SRR002322.
l = encReader.Reader.ReadInt32();
string secondIdPart = ae.GetString(encReader.Reader.ReadBytes(l)); //080317_CM-KID-LIV-2-REPEAT_0003: SPAZIO
//@SRX000571_SRR002322.18437692 080317_CM-KID-LIV-2-REPEAT_0003:7:330:466:87 length=36
//or
//@SRR029238.3 SOLEXAWS1_20FDNAAXX:1:1:737:1043
if (encReader.Reader.ReadBoolean())
{
idBuilder = firstIdPart + "{0} " + secondIdPart + "{1}:{2}:{3}:{4} length=" + length;
}
else
{
idBuilder = firstIdPart + "{0} " + secondIdPart + "{1}:{2}:{3}:{4}";
}
}
public EncodeIdDeCompresser(EncodedFastqReader encReader)
{
this.encReader = encReader;
int l = encReader.Reader.ReadInt32();
string firstIdPart = ae.GetString(encReader.Reader.ReadBytes(l)); //@HWUSI-EAS627_1
l = encReader.Reader.ReadInt32();
string paired = "";
if (l != 0)
{
paired = ae.GetString(encReader.Reader.ReadBytes(l)); // /1 (or /2)
}
//@HWUSI-EAS627_1:3:1:0:370/1 (or /2)
//@BILLIEHOLIDAY_3_FC30G08AAXX:1:1:0:1966
//Regex encode = new Regex(@"^(@[^:]+)(?:\d+:){3}\d+(\/[12])*$", RegexOptions.Singleline);
//ignoring:
//@080514_HWI-EAS229_0029_20768AAXX_5_1_120:242
//@TUPAC:1:1:5:710#0/1
idBuilder = firstIdPart + "{0}:{1}:{2}:{3}" + paired;
}
public static int Main(string[] args)
{
bool showHelp = false;
bool encodeIds = true;
bool encodeQualities = true;
string histogram = "";
int length = 0;
string filename = "";
string compression = "gzip";
string mode = "";
int cutoff = -1;
var p = new OptionSet()
{
{ "m|mode=", "the mode: encode|decode",
v => mode = v },
{ "l|length=", "the length of the reads",
(int v) => length = v },
{ "z|compression=", "the compression method to use: none|gzip|lzma - default is gzip",
v => compression = v },
{ "i|noId", "do not encode/decode Ids",
v => encodeIds = v == null },
{ "c|cutoff=", "cutoff to be used when encoding losing qualities -\n" +
"bases associated with a quality lower than the cutoff will be encoded as\n" +
"N",
(int v) => cutoff = v },
{ "q|noQuality", "do not encode/decode qualities - will use cutoff if given",
v => encodeQualities = v == null },
{ "s|qualityStats=", "create a SVG with a graph of fastq qualities and a .txt with quality values\n" +
"associated with counts, the given parameter is\n" +
"the desired basename of files (Warning: if they exist they will be REWRITTEN)\n" +
"will have effects alone or when in encode mode",
(string v) => histogram = v },
{ "h|help", "show this message and exit",
v => showHelp = v != null },
};
Boolean stop = false;
List <string> extraArgs = null;
string e = "";
try {
extraArgs = p.Parse(args);
}
catch (OptionException oe) {
stop = true;
e = oe.Message;
}
if ((length <= 0 || mode == "") && (histogram == ""))
{
Console.Error.WriteLine("Wrong (or no) length given or missing mode without the s option");
stop = true;
}
if (!stop && extraArgs.Count <= 1)
{
if (extraArgs.Count != 0)
{
filename = extraArgs[0];
}
}
else
{
stop = true;
}
if (mode == "decode" && histogram != "")
{
Console.Error.WriteLine("Warning! The option -s has no effect when decoding a file!");
}
if (showHelp)
{
ShowHelp(p);
return(0);
}
if (stop)
{
Console.WriteLine(e);
ShowHelp(p);
return(-1);
}
Stream output = Console.OpenStandardOutput();
if (compression == "lzma")
{
if (BitConverter.IsLittleEndian == false)
{
throw new Exception("Lzma compression not implemented for big endian machines.");
}
if (filename == "")
{
if (mode == "decode")
{
throw new InvalidOperationException("When decoding lzma files stdin cannot be used as input! " +
"Use a straight file instead.");
}
else
{
throw new InvalidOperationException("When encoding with lzma stdout cannot be used as output! " +
"Use a straight file instead.");
}
}
if (mode == "encode")
{
output = new FileStream(filename, FileMode.Create);
}
}
IFastqDeCompresser fdc = new FastqDeCompresser(length, encodeIds, encodeQualities);
try {
if (mode == "encode")
{
if (cutoff != -1 && !encodeQualities)
{
encodeQualities = true;
}
//we need to store qualities to put N in sequences when -c has been used!
BinaryWriter writer = null;
Stream zipWriter = null;
if (compression == "none")
{
writer = new BinaryWriter(output);
}
else if (compression == "gzip")
{
zipWriter = new GZipOutputStream(output, BUFFER);
writer = new BinaryWriter(zipWriter);
}
else if (compression == "lzma")
{
zipWriter = new LzmaStream(output, false);
writer = new BinaryWriter(zipWriter);
}
else
{
Console.Error.WriteLine("Wrong compression method given");
ShowHelp(p);
return(-1);
}
FastqReader reader = null;
if (filename != "" && compression != "lzma")
{
if (cutoff == -1)
{
reader = new FastqReader(filename, length, encodeIds, encodeQualities, histogram);
}
else
{
reader = new FastqCutoffReader(filename, length, encodeIds, encodeQualities, cutoff, histogram);
}
}
else
{
if (cutoff == -1)
{
reader = new FastqReader(Console.In, length, encodeIds, encodeQualities, histogram);
}
else
{
reader = new FastqCutoffReader(Console.In, length, encodeIds, encodeQualities, cutoff, histogram);
}
}
fdc.Compress(reader, writer);
reader.Close();
writer.Close();
}
else if (mode == "decode")
{
EncodedFastqReader reader = null;
StreamWriter writer = new StreamWriter(Console.OpenStandardOutput());
if (filename != "")
{
reader = new EncodedFastqReader(File.OpenRead(filename), compression);
}
else
{
reader = new EncodedFastqReader(Console.OpenStandardInput(), compression);
}
fdc.Decompress(reader, writer);
reader.Close();
writer.Close();
}
else
{
if (histogram == "")
{
Console.Error.WriteLine("Wrong or missing mode argument!");
ShowHelp(p);
return(-1);
}
else
{
FastqReader fq;
if (filename != "")
{
fq = new FastqReader(filename, histogram);
}
else
{
fq = new FastqReader(Console.In, histogram);
}
fq.Run();
fq.Close();
}
}
} catch (InvalidOperationException ioe) {
Console.Error.WriteLine(ioe.Message);
return(1);
} catch (FileNotFoundException fnfe) {
Console.Error.WriteLine("File {0} not found {1}!", filename, fnfe.Message);
return(1);
}
return(0);
}
public static int Main(string[] args)
{
bool showHelp = false;
bool encodeIds = true;
int length = 0;
string filename = "";
string compression = "gzip";
string mode = "";
string prefix = "";
string suffix = ".qfq";
int cutoff = -1;
bool encodeQualities = true;
var p = new OptionSet()
{
{ "m|mode=", "the mode: encode|decode",
v => mode = v },
{ "l|length=", "the length of the reads",
(int v) => length = v },
{ "z|compression=", "the compression method to use: none|gzip|lzma - default is gzip",
v => compression = v },
{ "p|prefix=", "the prefix for the output file",
v => prefix = v },
{ "i|noId", "do not encode/decode Ids",
v => encodeIds = v == null },
{ "c|cutoff=", "cutoff to be used when encoding losing qualities -\n" +
"bases associated with a quality lower than the cutoff will be encoded as\n" +
"N",
(int v) => cutoff = v },
{ "q|noQuality", "do not encode/decode qualities - will use cutoff if given",
v => encodeQualities = v == null },
{ "h|help", "show this message and exit",
v => showHelp = v != null },
};
bool stop = false;
List <string> extraArgs = null;
string e = "";
try {
extraArgs = p.Parse(args);
}
catch (OptionException oe) {
stop = true;
e = oe.Message;
}
if (length <= 0 || mode == "" || (mode == "encode" && prefix == ""))
{
stop = true;
}
if (mode == "encode" && cutoff != -1 && encodeQualities)
{
stop = true;
e = "In encode mode -c option can be used only with -q option!";
}
if (extraArgs.Count <= 1)
{
if (extraArgs.Count != 0)
{
filename = extraArgs[0];
}
}
else
{
stop = true;
}
if (showHelp)
{
ShowHelp(p);
return(0);
}
if (stop)
{
Console.WriteLine(e);
ShowHelp(p);
return(-1);
}
string outputFile = prefix + suffix;
if (compression == "gzip")
{
outputFile += ".gz";
}
else if (compression == "lzma")
{
outputFile += ".lzma";
}
IFastqDeCompresser fdc = new FastqDeCompresser(length, encodeIds, encodeQualities);
try {
if (mode == "encode")
{
FileStream outStream = new FileStream(outputFile, FileMode.Create);
BinaryWriter writer = null;
Stream zipWriter = null;
try {
if (compression == "none")
{
writer = new BinaryWriter(outStream);
}
else if (compression == "gzip")
{
zipWriter = new GZipOutputStream(outStream);
writer = new BinaryWriter(zipWriter);
}
else if (compression == "lzma")
{
zipWriter = new LzmaEncodeStream(outStream);
writer = new BinaryWriter(zipWriter);
}
else
{
Console.Error.WriteLine("Wrong compression method given");
ShowHelp(p);
return(-1);
}
FastqReader reader = null;
if (filename != "")
{
if (cutoff == -1)
{
reader = new FastqReader(filename, length);
}
else
{
reader = new FastqCutoffReader(filename, length, cutoff);
}
}
else
{
if (cutoff == -1)
{
reader = new FastqReader(Console.In, length);
}
else
{
reader = new FastqCutoffReader(Console.In, length, cutoff);
}
}
fdc.Compress(reader, writer);
reader.Close();
} finally {
writer.Close();
outStream.Close();
//XXX should close correct streams!
}
}
else if (mode == "decode")
{
EncodedFastqReader reader = new EncodedFastqReader(File.OpenRead(outputFile), compression);
StreamWriter writer = new StreamWriter(Console.OpenStandardOutput());
try {
fdc.Decompress(reader, writer);
} finally {
reader.Close();
writer.Close();
}
}
else
{
ShowHelp(p);
return(-1);
}
} catch (InvalidOperationException ioe) {
Console.Error.WriteLine(ioe.Message);
return(1);
} catch (FileNotFoundException fnfe) {
Console.Error.WriteLine("File {0} not found {1}!", filename, fnfe.Message);
return(1);
} /*finally {
* // TODO ASK
* }*/
return(0);
}
/* Main decompression method that decodes the compressed file and
* directly write the obtained fastq in the given StreamWriter.
*/
public void Decompress(EncodedFastqReader reader, StreamWriter writer)
{
long IdByte = 0;
long seqI = 0;
int s = 0;
long qualI = 0;
int q = 0;
int nSeq = 0;
int howmany = 0;
char which = ' ';
byte encoded;
//continuations variables
int continueSequenceRunLength = 0;
char[] continueSequenceChar = new char[] { ' ', ' ' };
//0 - the rl char or the second char of the triplet across reads
//1 - the rl char or the third char of the triplet across reads
int continueQualityRunLength = 0;
char continueQualityChar = ' ';
ChooseIddc(reader);
writer.WriteLine(iddc.GetNextID(ref IdByte));
while (reader.HasSeqLeft(seqI, 1) || continueSequenceRunLength != 0 || continueSequenceChar[0] != ' ' ||
(encodeQualities && reader.HasQLeft(qualI, 1)) || continueQualityRunLength != 0)
{
q = 0;
s = 0;
while (s < length)
{
if (continueSequenceRunLength != 0)
{
while (continueSequenceRunLength > 0 && s < length)
{
s++;
continueSequenceRunLength--;
writer.Write(continueSequenceChar[0]);
}
if (continueSequenceRunLength == 0)
{
continueSequenceChar[0] = ' ';
}
}
else if (continueSequenceChar[0] != ' ')
{
//we assume that 1 or 2 char(s) will always fit in the new read
//ie reads will always be longer than 2
writer.Write(continueSequenceChar[0]);
s++;
if (continueSequenceChar[1] != ' ')
{
writer.Write(continueSequenceChar[1]);
s++;
}
continueSequenceChar[0] = ' ';
continueSequenceChar[1] = ' ';
}
else if (reader.HasSeqLeft(seqI, 1))
{
encoded = reader.GetSeqByte(seqI);
seqI++;
if ((encoded & 128) == 128) //run length
{
encoded = (byte)(127 & encoded);
howmany = (encoded >> 3) + 4;
which = Bases[(int)(encoded & 7)];
int i = 0;
while (i < howmany && s < length)
{
i++;
s++;
writer.Write(which);
}
if (i < howmany)
{
continueSequenceChar[0] = which;
continueSequenceRunLength = howmany - i;
}
}
else //three bases
{
string triplet = decoding[(int)encoded];
int k = 0;
while (s < length && k < 3)
{
writer.Write(triplet[k++]);
s++;
}
int i = 0;
while (k < 3)
{
continueSequenceChar[i] = triplet[k];
k++;
i++;
}
}
}
}
nSeq++;
if (encodeQualities)
{
writer.WriteLine("\n+");
}
while (encodeQualities && q < length)
{
if (continueQualityRunLength != 0)
{
while (continueQualityRunLength > 0 && q < length)
{
q++;
continueQualityRunLength--;
writer.Write(continueQualityChar);
}
if (continueQualityRunLength == 0)
{
continueQualityChar = ' ';
}
}
else if (reader.HasQLeft(qualI, 1))
{
encoded = reader.GetQualByte(qualI);
qualI++;
if ((encoded & 128) != 128) //single quality data
{
which = Convert.ToChar(encoded);
writer.Write(which);
q++;
}
else //run length
{
encoded = (byte)(127 & encoded);
which = Convert.ToChar(encoded);
howmany = (int)reader.GetQualByte(qualI);
qualI++;
int i = 0;
while (i < howmany && q < length)
{
i++;
q++;
writer.Write(which);
}
if (i < howmany)
{
continueQualityRunLength = howmany - i;
continueQualityChar = which;
}
}
}
}
if (reader.HasSeqLeft(seqI, 1) || continueSequenceRunLength != 0)
{
//if we have got a sequence run length it cannot be padding and if we have
//a continuation derived for a triplet we will have sequences left if it's
//not a padding
writer.WriteLine("\n" + iddc.GetNextID(ref IdByte));
if (seqI % 10000 == 0)
{
Spin("Decoding...");
}
}
else if (!reader.HasSeqLeft(seqI, 1) && continueSequenceChar[0] != ' ')
{
break;
}
}
writer.WriteLine();
Console.Error.WriteLine();
}
public PlainIdDeCompresser(EncodedFastqReader encReader)
{
this.encReader = encReader;
}