internal static bool IsSimpleSequence([NotNull] this IVcfVariant variant, out uint absoluteDiff,
out bool sharedFirstBase, out bool sharedLastBase, bool isTrimmed)
{
absoluteDiff = default;
sharedFirstBase = false;
sharedLastBase = false;
if (variant.Alts.Count == 0)
{
return(false);
}
if (variant.IsAltSimpleSequence(0))
{
absoluteDiff = (uint)Math.Max(variant.Ref.Length, variant.Alts[0].Length);
sharedFirstBase = variant.Ref[0].Letter == variant.Alts[0][0];
sharedLastBase = variant.Ref.Last().Letter == variant.Alts[0].Last();
if (isTrimmed && sharedFirstBase && sharedLastBase && (variant.Ref.Length == 1 || variant.Alts[0].Length == 1))
{
sharedLastBase = false; // corner case like chr1 1 A AA would be true for both.
}
if (isTrimmed && sharedFirstBase && sharedLastBase)
{
throw new InvalidDataException(
"Somehow we got a variant that after trimming, shares first and last base: " + variant);
}
if (sharedFirstBase || sharedLastBase)
{
absoluteDiff--;
}
return(true);
}
// always assume the first base is shared in symbolic alleles.
sharedFirstBase = true;
// and last base never shared.
sharedLastBase = false;
absoluteDiff = default;
return(false);
}
internal static IInterval <uint> GetInsertionInterval([NotNull] IVcfVariant first)
=> first.IsAltSimpleSequence(0)
? first.ToBedInterval(false, out _, out _)
: first.TryGetSvLength(out var svLen) != null
