Exemplo n.º 1
0
        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);
        }
Exemplo n.º 2
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);
        }