/// <summary>
/// Parses a line from a VCF File
/// </summary>
/// <param name="parts">An array of length >8 where the 9th element contains unsplit genotype data (if present)</param>
/// <param name="includeGenotypes"> Whether or not to also parse the genotype data </param>
/// <returns></returns>
private VariantContext parseVCFLine(string[] parts, bool includeGenotypes)
{
VariantContextBuilder builder = new VariantContextBuilder();
builder.Source = Name;
// increment the line count
lineNo++;
// parse out the required fields
string chr = GetCachedString(parts [0]);
builder.Contig = chr;
int pos = -1;
try {
pos = Convert.ToInt32(parts [1]);
} catch (FormatException e) {
generateException(parts [1] + " is not a valid start position in the VCF format");
}
builder.Start = pos;
if (parts [2].Length == 0)
{
generateException("The VCF specification requires a valid ID field");
}
else if (parts [2].Equals(VCFConstants.EMPTY_ID_FIELD))
{
builder.ID = VCFConstants.EMPTY_ID_FIELD;
}
else
{
builder.ID = parts [2];
}
string refe = GetCachedString(parts [3].ToUpper());
string alts = GetCachedString(parts [4].ToUpper());
builder.Log10PError = parseQual(parts [5]);
string filterStr = GetCachedString(parts [6]);
var filters = filterHash [filterStr];
if (filters != null) //means filter data present
{
builder.SetFilters(filters.Hash);
}
IDictionary <string, object> attrs = parseInfo(parts [7]);
builder.Attributes = attrs;
if (attrs.ContainsKey(VCFConstants.END_KEY))
{
// update stop with the end key if provided
try {
builder.Stop = Convert.ToInt32(attrs [VCFConstants.END_KEY].ToString());
} catch (Exception e) {
generateException("the END value in the INFO field is not valid");
}
}
else
{
builder.Stop = (pos + refe.Length - 1);
}
// get our alleles, filters, and setup an attribute map
IList <Allele> alleles = parseAlleles(refe, alts, lineNo);
builder.SetAlleles(alleles);
// do we have genotyping data
if (parts.Length > NUM_STANDARD_FIELDS && includeGenotypes)
{
int nGenotypes = header.NGenotypeSamples;
LazyGenotypesContext lazy = new LazyGenotypesContext(this, alleles, chr, pos, parts [8], nGenotypes);
// did we resort the sample names? If so, we need to load the genotype data
if (!header.SamplesWereAlreadySorted)
{
lazy.Decode();
}
builder.SetGenotypes(lazy, false);
}
VariantContext vc = null;
try {
vc = builder.make();
} catch (Exception e) {
generateException(e.Message);
}
return(vc);
}
/// <summary>
/// Parses a line from a VCF File
/// </summary>
/// <param name="parts">An array of length >8 where the 9th element contains unsplit genotype data (if present)</param>
/// <param name="includeGenotypes"> Whether or not to also parse the genotype data </param>
/// <returns></returns>
private VariantContext parseVCFLine (string[] parts, bool includeGenotypes)
{
VariantContextBuilder builder = new VariantContextBuilder ();
builder.Source = Name;
// increment the line count
lineNo++;
// parse out the required fields
string chr = GetCachedString (parts [0]);
builder.Contig = chr;
int pos = -1;
try {
pos = Convert.ToInt32 (parts [1]);
} catch (FormatException e) {
generateException (parts [1] + " is not a valid start position in the VCF format");
}
builder.Start = pos;
if (parts [2].Length == 0) {
generateException ("The VCF specification requires a valid ID field");
} else if (parts [2].Equals (VCFConstants.EMPTY_ID_FIELD)) {
builder.ID = VCFConstants.EMPTY_ID_FIELD;
} else {
builder.ID = parts [2];
}
string refe = GetCachedString (parts [3].ToUpper ());
string alts = GetCachedString (parts [4].ToUpper ());
builder.Log10PError = parseQual (parts [5]);
string filterStr = GetCachedString (parts [6]);
var filters = filterHash [filterStr];
if (filters != null) {//means filter data present
builder.SetFilters (filters.Hash);
}
IDictionary<string, object> attrs = parseInfo (parts [7]);
builder.Attributes = attrs;
if (attrs.ContainsKey (VCFConstants.END_KEY)) {
// update stop with the end key if provided
try {
builder.Stop = Convert.ToInt32 (attrs [VCFConstants.END_KEY].ToString ());
} catch (Exception e) {
generateException ("the END value in the INFO field is not valid");
}
} else {
builder.Stop = (pos + refe.Length - 1);
}
// get our alleles, filters, and setup an attribute map
IList<Allele> alleles = parseAlleles (refe, alts, lineNo);
builder.SetAlleles (alleles);
// do we have genotyping data
if (parts.Length > NUM_STANDARD_FIELDS && includeGenotypes) {
int nGenotypes = header.NGenotypeSamples;
LazyGenotypesContext lazy = new LazyGenotypesContext (this, alleles, chr, pos, parts [8], nGenotypes);
// did we resort the sample names? If so, we need to load the genotype data
if (!header.SamplesWereAlreadySorted) {
lazy.Decode ();
}
builder.SetGenotypes (lazy, false);
}
VariantContext vc = null;
try {
vc = builder.make ();
} catch (Exception e) {
generateException (e.Message);
}
return vc;
}
