コード例 #1
0
        /// <summary>
        /// create a VCF filter header line
        /// </summary>
        /// <param name="key">            the key for this header line </param>
        /// <param name="name">           the name for this header line </param>
        /// <param name="description">    description for this header line </param>
        public VCFSimpleHeaderLine(string key, string name, string description) : base(key, "")
        {
            IDictionary <string, string> map = new OrderedGenericDictionary <string, string>();

            map["Description"] = description;
            initialize(name, map);
        }
コード例 #2
0
        /// <summary>
        /// make a string representation of this header line </summary>
        /// <returns> a string representation </returns>
        protected internal override string toStringEncoding()
        {
            IDictionary <string, object> map = new OrderedGenericDictionary <string, object>();

            map["ID"] = name;
            object number;

            switch (countType)
            {
            case Bio.VCF.VCFHeaderLineCount.A:
                number = VCFConstants.PER_ALTERNATE_ALLELE_COUNT;
                break;

            case Bio.VCF.VCFHeaderLineCount.R:
                number = VCFConstants.PER_ALLELE_COUNT;
                break;

            case Bio.VCF.VCFHeaderLineCount.G:
                number = VCFConstants.PER_GENOTYPE_COUNT;
                break;

            case Bio.VCF.VCFHeaderLineCount.UNBOUNDED:
                number = VCFConstants.UNBOUNDED_ENCODING_v4;
                break;

            case Bio.VCF.VCFHeaderLineCount.INTEGER:
            default:
                number = count;
                break;
            }
            map["Number"]      = number;
            map["Type"]        = type;
            map["Description"] = description;
            return(lineType.ToString() + "=" + VCFHeaderLine.toStringEncoding(map));
        }
コード例 #3
0
        protected internal override string toStringEncoding()
        {
            OrderedGenericDictionary <string, string> map = new OrderedGenericDictionary <string, string>();

            map["ID"] = name;
            map.putAll(genericFields);
            return(Key + "=" + VCFHeaderLine.toStringEncoding(map));
        }
コード例 #4
0
        /// <summary>
        /// parse a VCF4 line </summary>
        /// <param name="valueLine"> the line </param>
        /// <returns> a mapping of the tags parsed out </returns>
        public virtual IDictionary <string, string> parseLine(string valueLine, params string[] expectedTagOrder)
        {
            // our return map
            OrderedGenericDictionary <string, string> ret = new OrderedGenericDictionary <string, string>();

            // a builder to store up characters as we go
            StringBuilder builder = new StringBuilder();

            // store the key when we're parsing out the values
            string key = "";

            // where are we in the stream of characters?
            int index = 0;

            // are we inside a quotation? we don't special case ',' then
            bool inQuote = false;

            // a little switch machine to parse out the tags. Regex ended up being really complicated and ugly [yes, but this machine is getting ugly now... MAD]
            foreach (char c in valueLine.ToCharArray())
            {
                if (c == '\"')
                {
                    inQuote = !inQuote;
                }
                else if (inQuote)
                {
                    builder.Append(c);
                }
                else
                {
                    switch (c)
                    {
                    case ('<'):                              // if we see a open bracket at the beginning, ignore it
                        if (index == 0)
                        {
                            break;
                        }
                        else
                        {
                            goto case '>';
                        }

                    case ('>'):                              // if we see a close bracket, and we're at the end, add an entry to our list
                        if (index == valueLine.Length - 1)
                        {
                            ret[key] = builder.ToString().Trim();
                        }
                        break;

                    case ('='):                              // at an equals, copy the key and reset the builder
                        key     = builder.ToString().Trim();
                        builder = new StringBuilder();
                        break;

                    case (','):                              // drop the current key value to the return map
                        ret[key] = builder.ToString().Trim();
                        builder  = new StringBuilder();
                        break;

                    default:                             // otherwise simply append to the current string
                        builder.Append(c);
                        break;
                    }
                }

                index++;
            }

            // validate the tags against the expected list
            index = 0;
            if (expectedTagOrder != null)
            {
                if (ret.Count > expectedTagOrder.Length)
                {
                    throw new VCFParsingError("unexpected tag count " + ret.Count + " in line " + valueLine);
                }
                foreach (string str in ret.Keys)
                {
                    if (!expectedTagOrder[index].Equals(str))
                    {
                        throw new VCFParsingError("Unexpected tag " + str + " in line " + valueLine);
                    }
                    index++;
                }
            }
            return(ret);
        }
コード例 #5
0
        public virtual IDictionary <string, string> parseLine(string valueLine, params string[] expectedTagOrder)
        {
            // our return map
            OrderedGenericDictionary <string, string> ret = new OrderedGenericDictionary <string, string>();

            // a builder to store up characters as we go
            StringBuilder builder = new StringBuilder();

            // where are we in the stream of characters?
            int index = 0;
            // where in the expected tag order are we?
            int tagIndex = 0;

            // are we inside a quotation? we don't special case ',' then
            bool inQuote = false;

            // a little switch machine to parse out the tags. Regex ended up being really complicated and ugly
            foreach (char c in valueLine.ToCharArray())
            {
                switch (c)
                {
                case ('\"'):                          // a quote means we ignore ',' in our strings, keep track of it
                    inQuote = !inQuote;
                    break;

                case (','):                          // drop the current key value to the return map
                    if (!inQuote)
                    {
                        ret[expectedTagOrder[tagIndex++]] = builder.ToString();
                        builder = new StringBuilder();
                        break;
                    }
                    else
                    {
                        goto default;
                    }

                default:                         // otherwise simply append to the current string
                    builder.Append(c);
                    break;
                }
                index++;
            }
            ret[expectedTagOrder[tagIndex++]] = builder.ToString();

            // validate the tags against the expected list
            index = 0;
            if (tagIndex != expectedTagOrder.Length)
            {
                throw new System.ArgumentException("Unexpected tag count " + tagIndex + ", we expected " + expectedTagOrder.Length);
            }
            foreach (string str in ret.Keys)
            {
                if (!expectedTagOrder[index].Equals(str))
                {
                    throw new System.ArgumentException("Unexpected tag " + str + " in string " + valueLine);
                }
                index++;
            }
            return(ret);
        }