/// <summary>
/// Extracts a exac item(s) from the specified VCF line.
/// </summary>
/// <param name="vcfline"></param>
/// <returns></returns>
public List <ExacItem> ExtractItems(string vcfline)
{
if (vcfline == null)
{
return(null);
}
var splitLine = vcfline.Split('\t'); // we don't care about the many fields after info field
if (splitLine.Length < 8)
{
return(null);
}
Clear();
var chromosome = splitLine[VcfCommon.ChromIndex];
if (!_refChromDict.ContainsKey(chromosome))
{
return(null);
}
var chrom = _refChromDict[chromosome];
var position = int.Parse(splitLine[VcfCommon.PosIndex]); //we have to get it from RSPOS in info
var refAllele = splitLine[VcfCommon.RefIndex];
var altAlleles = splitLine[VcfCommon.AltIndex].Split(',');
var infoFields = splitLine[VcfCommon.InfoIndex];
// parses the info fields and extract frequencies, coverage, num samples.
ParseInfoField(infoFields);
if (_anAdj == 0)
{
return(null);
}
var exacItemsList = new List <ExacItem>();
for (int i = 0; i < altAlleles.Length; i++)
{
exacItemsList.Add(new ExacItem(
chrom,
position,
refAllele,
altAlleles[i],
ComputingUtilities.GetCoverage(_totalDepth, _anAdj / 2.0),
//(int) Math.Round(_totalDepth*1.0/ (_anAdj/2.0), MidpointRounding.AwayFromZero),//to be consistant with evs, we use integer values for coverage
_anAdj, _anAfr, _anAmr, _anEas, _anFin, _anNfe, _anOth, _anSas,
GetAlleleCount(_acAdj, i), GetAlleleCount(_acAfr, i), GetAlleleCount(_acAmr, i), GetAlleleCount(_acEas, i),
GetAlleleCount(_acFin, i), GetAlleleCount(_acNfe, i), GetAlleleCount(_acOth, i), GetAlleleCount(_acSas, i))
);
}
return(exacItemsList);
}
public string GetJsonString()
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("allAf", ComputingUtilities.ComputeFrequency(_alleleNum, _alleleCount), false);
jsonObject.AddIntValue("allAn", _alleleNum);
jsonObject.AddIntValue("allAc", _alleleCount);
jsonObject.AddIntValue("allHc", _homCount);
if (_failedFilter)
{
jsonObject.AddBoolValue("failedFilter", true);
}
return(sb.ToString());
}
