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 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 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])));
}
