private VariantContext decodeLine(string line, bool includeGenotypes)
{
// the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
if (line.StartsWith(VCFHeader.HEADER_INDICATOR))
{
//TODO: Possibly raise exception? At least in one scenario, the VCF header has already been parsed before this is called
//seems like this should always be true based on statement below
throw new VCFParsingError("While decoding genotype lines came across a commented header line. Problem is with line:\n " + line);
}
// our header cannot be null, we need the genotype sample names and counts
if (header == null)
{
throw new VCFParsingError("VCF Header cannot be null when decoding a record");
}
//I think this is not necessary
int parseSize = Math.Min(header.ColumnCount, NUM_STANDARD_FIELDS + 1);
//TODO: Original bit of code here could do lazy genotype initalization and so could split off the
//first 8 columns, leaving any genotype data still lumped together in the 9th column (if present).
// string[] parts=line.Split(VCFConstants.FIELD_SEPARATOR_CHAR_AS_ARRAY,parseSize,StringSplitOptions.None);
string[] parts = FastStringUtils.Split(line, VCFConstants.FIELD_SEPARATOR_CHAR, parseSize, StringSplitOptions.None);
//ND - Modified this heavily, as it is imposssible for header to be null at this stage.
// if we have don't have a header, or we have a header with no genotyping data check that we have eight columns.
// Otherwise check that we have nine (normal colummns + genotyping data)
if ((!header.hasGenotypingData() && parts.Length != NUM_STANDARD_FIELDS) ||
(header.hasGenotypingData() && parts.Length != (NUM_STANDARD_FIELDS + 1)))
{
throw new VCFParsingError("Line " + lineNo + ": there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) + " tokens, and saw " + parts.Length + " )");
}
return(parseVCFLine(parts, includeGenotypes));
}
/// <summary>
/// Create a genotype map
/// </summary>
/// <param name="str"> the string </param>
/// <param name="alleles"> the list of alleles </param>
/// <returns> a mapping of sample name to genotype object </returns>
public LazyGenotypesContext.LazyData CreateGenotypeMap(string str, IList <Allele> alleles, string chr, int pos)
{
if (genotypeParts == null)
{
genotypeParts = new String[header.ColumnCount - NUM_STANDARD_FIELDS];
}
try {
FastStringUtils.Split(str, VCFConstants.FIELD_SEPARATOR_CHAR, genotypeParts);
} catch (Exception e) {
throw new VCFParsingError("Could not parse genotypes, was expecting " + (genotypeParts.Length - 1).ToString() + " but found " + str.Split(VCFConstants.FIELD_SEPARATOR_CHAR).Length.ToString(), e);
}
List <Genotype> genotypes = new List <Genotype> (genotypeParts.Length);
// get the format keys
//int nGTKeys = ParsingUtils.Split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
string[] genotypeKeyArray = genotypeParts [0].Split(VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
int genotypeAlleleLocation = Array.IndexOf(genotypeKeyArray, VCFConstants.GENOTYPE_KEY);
if (version != VCFHeaderVersion.VCF4_1 && genotypeAlleleLocation == -1)
{
generateException("Unable to find the GT field for the record; the GT field is required in VCF4.0");
}
// clear out our allele mapping
alleleMap.Clear();
GenotypeBuilder gb = new GenotypeBuilder();
// cycle through the genotype strings
for (int genotypeOffset = 1; genotypeOffset < genotypeParts.Length; genotypeOffset++)
{
Genotype curGenotype;
string sampleName = header.GenotypeSampleNames [genotypeOffset - 1];
var currentGeno = genotypeParts [genotypeOffset];
//shortcut for null alleles
if (currentGeno == "./.")
{
curGenotype = GenotypeBuilder.CreateMissing(sampleName, 2);
}
else if (currentGeno == ".")
{
curGenotype = GenotypeBuilder.CreateMissing(sampleName, 1);
}
else
{
gb.Reset(false);
gb.SampleName = sampleName;
string[] GTValueArray = FastStringUtils.Split(currentGeno, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR, int.MaxValue, StringSplitOptions.None);
// cycle through the sample names
// check to see if the value list is longer than the key list, which is a problem
if (genotypeKeyArray.Length < GTValueArray.Length)
{
generateException("There are too many keys for the sample " + sampleName + ", line is: keys = " + genotypeParts [0] + ", values = " + genotypeParts [genotypeOffset]);
}
if (genotypeAlleleLocation > 0)
{
generateException("Saw GT field at position " + genotypeAlleleLocation + ", but it must be at the first position for genotypes when present");
}
//TODO: THIS IS A DAMNED MESS
//Code loops over all fields in the key and decodes them, adding them as information to the genotype builder, which then makes it.
if (genotypeKeyArray.Length > 0)
{
gb.MaxAttributes(genotypeKeyArray.Length - 1);
for (int i = 0; i < genotypeKeyArray.Length; i++)
{
string gtKey = genotypeKeyArray [i];
if (i >= GTValueArray.Length)
{
break;
}
// todo -- all of these on the fly parsing of the missing value should be static constants
if (gtKey == VCFConstants.GENOTYPE_FILTER_KEY)
{
IList <string> filters = parseFilters(GetCachedString(GTValueArray [i]));
if (filters != null)
{
gb.SetFilters(filters.ToList());
}
}
else if (GTValueArray [i] == VCFConstants.MISSING_VALUE_v4)
{
// don't add missing values to the map
}
else
{
if (gtKey == VCFConstants.GENOTYPE_QUALITY_KEY)
{
if (GTValueArray [i] == VCFConstants.MISSING_GENOTYPE_QUALITY_v3)
{
gb.noGQ();
}
else
{
gb.GQ = ((int)Math.Round(Convert.ToDouble(GTValueArray [i])));
}
}
else if (gtKey == VCFConstants.GENOTYPE_ALLELE_DEPTHS)
{
gb.AD = (decodeInts(GTValueArray [i]));
}
else if (gtKey == VCFConstants.GENOTYPE_PL_KEY)
{
gb.PL = (decodeInts(GTValueArray [i]));
}
else if (gtKey == VCFConstants.GENOTYPE_LIKELIHOODS_KEY)
{
gb.PL = (GenotypeLikelihoods.fromGLField(GTValueArray [i]).AsPLs);
}
else if (gtKey.Equals(VCFConstants.DEPTH_KEY))
{
gb.DP = (Convert.ToInt32(GTValueArray [i]));
}
else
{
gb.AddAttribute(gtKey, GTValueArray [i]);
}
}
}
}
List <Allele> GTalleles;
if (genotypeAlleleLocation == -1)
{
GTalleles = new List <Allele> (0);
}
else
{
GTalleles = parseGenotypeAlleles(GTValueArray [genotypeAlleleLocation], alleles, alleleMap);
}
gb.Alleles = GTalleles;
gb.Phased = genotypeAlleleLocation != -1 && GTValueArray [genotypeAlleleLocation].IndexOf(VCFConstants.PHASED_AS_CHAR) != -1;
// add it to the list
try {
curGenotype = gb.Make();
} catch (Exception e) {
throw new VCFParsingError(e.Message + ", at position " + chr + ":" + pos);
}
}
genotypes.Add(curGenotype);
}
return(new LazyGenotypesContext.LazyData(genotypes, header.SampleNamesInOrder, header.SampleNameToOffset));
}
