Example #1
0
            internal static IWittyerVariant Create([NotNull] IVcfVariant baseVariant,
                                                   string sample, double percentageDistance, uint basepairDistance,
                                                   IReadOnlyList <uint> bins, WittyerVariantType svType)
            {
                if (svType == WittyerVariantType.Invalid)
                {
                    throw new InvalidDataException(
                              $"Invalid {VcfConstants.SvTypeKey} in variant: \n{baseVariant}\nNot sure why you got here though. Check with a witty.er developer!");
                }

                var end          = baseVariant.Position + baseVariant.GetSvLength();
                var baseInterval = BedInterval.Create(baseVariant.Position, end);

                var borderInterval =
                    baseVariant.Position.CalculateBorderInterval(baseInterval,
                                                                 baseVariant.ParseCi(WittyerConstants.Cipos),
                                                                 percentageDistance, basepairDistance);

                // wittyerVariant should all have end border, it's a matter of how to find it,
                // either END key in INFO field, sort out through SVLEN or other ways, details can be defined in FindEndBorder() later
                var endInterval = (end - 1).CalculateBorderInterval(baseInterval,
                                                                    baseVariant.ParseCi(WittyerConstants.Ciend),
                                                                    percentageDistance, basepairDistance);

                var posContigAndInterval =
                    ContigAndInterval.Create(baseVariant.Contig, borderInterval.Start, borderInterval.Stop + 1);
                var endContigAndInterval =
                    ContigAndInterval.Create(baseVariant.Contig, endInterval.Start, endInterval.Stop + 1);

                return(Create(baseVariant, baseInterval, svType, posContigAndInterval,
                              Winner.Create(svType, baseInterval, bins), new List <OverlapAnnotation>(),
                              WittyerSample.CreateOverall(baseVariant, sample, svType == WittyerVariantType.CopyNumberReference),
                              endContigAndInterval));
            }