internal static string ToString([NotNull] IVcfVariant variant, bool?isTruth)
{
var ret = variant.ToStrings().Take(FormatIndex).ToList();
// order the info fields
if (ret[InfoIndex] != MissingValueString)
{
ret[InfoIndex] = variant.Info.OrderBy(kvp => kvp.Key)
.Select(kvp => kvp.Value.IsNullOrEmpty()
? kvp.Key
: $"{kvp.Key}{InfoFieldKeyValueDelimiter}{kvp.Value}")
.StringJoin(InfoFieldDelimiter);
}
// add format column
ret.Add(variant.Samples[0].SampleDictionary.Keys.StringJoin(SampleFieldDelimiter));
if (isTruth == null)
{
var values = variant.Samples[0].SampleDictionary.Values;
ret.Add(values.All(it => string.IsNullOrEmpty(it) || it == MissingValueString)
? MissingValueString
: values.StringJoin(SampleFieldDelimiter));
}
else if (isTruth.Value)
{
ret.Add(variant.Samples[0].SampleDictionary.Values.StringJoin(SampleFieldDelimiter));
ret.Add(MissingValueString);
}
else
{
ret.Add(MissingValueString);
ret.Add(variant.Samples[1].SampleDictionary.Values.StringJoin(SampleFieldDelimiter));
}
return(ret.StringJoin(ColumnDelimiter));
}
internal static IInterval <uint> ConvertPositionToCiInterval(
this uint position, [NotNull] IVcfVariant variant, [NotNull] string ciInfoTag)
{
if (!variant.Info.TryGetValue(ciInfoTag, out var posString))
{
return(BedInterval.Create(position > 0 ? position - 1 : 0, position == 0 ? 1 : position));
}
var split = posString.Split(WittyerConstants.InfoValueDel);
if (split.Length != 2)
{
throw VcfVariantFormatException.Create(variant.ToString(), ImmutableHashSet.Create(VcfColumn.Info),
$"Invalid {ciInfoTag} found: {posString}", variant.ToStrings().ToList().AsReadOnly());
}
var parsedStart = GetParsedAbsValue(split[0]);
if (parsedStart == null)
{
throw new InvalidOperationException($"Failed to parse {ciInfoTag}={posString}!");
}
var parsedStop = GetParsedAbsValue(split[1]);
if (parsedStop == null)
{
throw new InvalidOperationException($"Failed to parse {ciInfoTag}={posString}!");
}
var(start, stop) = ConvertPositionToCiInterval(position, (parsedStart.Value, parsedStop.Value));
return(BedInterval.Create(start, stop));
uint?GetParsedAbsValue(string val)
=> !int.TryParse(val, out var parsed) ? (uint?)null : (uint)(parsed < 0 ? -parsed : parsed);
}
internal static IInterval <uint> ConvertPositionToCiInterval(
this uint position, [NotNull] IVcfVariant variant, [NotNull] string ciInfoTag)
{
if (!variant.Info.TryGetValue(ciInfoTag, out var posString))
{
return(BedInterval.Create(position > 0 ? position - 1 : 0, position == 0 ? 1 : position));
}
var split = posString.Split(WittyerConstants.InfoValueDel);
if (split.Length != 2)
{
throw VcfVariantFormatException.Create(variant.ToString(), ImmutableHashSet.Create(VcfColumn.Info),
$"Invalid {ciInfoTag} found: {posString}", variant.ToStrings().ToList().AsReadOnly());
}
var(start, stop) = ConvertPositionToCiInterval(position, (GetParsedAbsValue(split[0]), GetParsedAbsValue(split[1])));
return(BedInterval.Create(start, stop));
uint GetParsedAbsValue(string val)
{
var parsed = int.Parse(val);
return((uint)(parsed < 0 ? -parsed : parsed));
}
}
internal static InclusiveInterval <int> ParseCi([NotNull] this IVcfVariant variant, string tag)
{
if (!variant.Info.TryGetValue(tag, out var posString))
{
return(new InclusiveInterval <int>(0, 0));
}
var split = posString.Split(WittyerConstants.InfoValueDel);
if (split.Length != 2)
{
throw VcfVariantFormatException.Create(variant.ToString(), ImmutableHashSet.Create(VcfColumn.Info),
$"Invalid {tag} found: {posString}", variant.ToStrings().ToList().AsReadOnly());
}
return(new InclusiveInterval <int>(int.Parse(split[0]), int.Parse(split[1])));
}