/// <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);
}
/// <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));
}
protected internal override string toStringEncoding()
{
OrderedGenericDictionary <string, string> map = new OrderedGenericDictionary <string, string>();
map["ID"] = name;
map.putAll(genericFields);
return(Key + "=" + VCFHeaderLine.toStringEncoding(map));
}
/// <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);
}
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);
}
