public void GenerateWhatAndWhyWorksWithCnSample(bool isAlleleMatch, uint posStart, uint posEnd, uint endStart, uint endEnd,
bool isGtMatch, uint cn, MatchEnum matchResult, FailedReason reasonResult)
{
var originalVariant = GetOriginalCnvGtVariant();
var otherVariant =
SetupBasicVariant(isAlleleMatch ? PrimaryContigAndInterval : PrimaryFailedContigAndInterval);
otherVariant.SetupGet(v => v.PosInterval).Returns(ContigAndInterval.Create(PrimaryContig, posStart, posEnd));
otherVariant.SetupGet(v => v.EndInterval).Returns(ContigAndInterval.Create(PrimaryContig, endStart, endEnd));
var otherSample = new Mock <IWittyerGenotypedCopyNumberSample>();
var gt = new Mock <IGenotypeInfo>();
if (originalVariant.Sample is IWittyerGenotypedSample gtSample)
{
gt.Setup(g => g.Equals(gtSample.Gt)).Returns(isGtMatch);
}
otherSample.SetupGet(s => s.Gt).Returns(gt.Object);
otherSample.SetupGet(s => s.Cn).Returns(cn);
otherVariant.SetupGet(v => v.Sample).Returns(otherSample.Object);
var actual = OverlappingUtils.GenerateWhatAndWhy(otherVariant.Object, new List <FailedReason>(),
originalVariant, OverlappingUtils.IsVariantAlleleMatch, false);
Assert.Equal((matchResult, reasonResult), actual);
}
/// <summary>
/// Initializes a new instance of the <see cref="InputCollectionFilter" /> class.
/// </summary>
/// <param name="input">Collection of strings to filter (required).</param>
/// <param name="match">Match type (required) (default to MatchEnum.Any).</param>
/// <param name="keywords">Keywords (separate multiple values with commas) (required).</param>
public InputCollectionFilter(List <string> input = default(List <string>), MatchEnum match = MatchEnum.Any, string keywords = default(string))
{
// to ensure "input" is required (not null)
if (input == null)
{
throw new InvalidDataException("input is a required property for InputCollectionFilter and cannot be null");
}
else
{
this.Input = input;
}
// to ensure "match" is required (not null)
if (match == null)
{
throw new InvalidDataException("match is a required property for InputCollectionFilter and cannot be null");
}
else
{
this.Match = match;
}
// to ensure "keywords" is required (not null)
if (keywords == null)
{
throw new InvalidDataException("keywords is a required property for InputCollectionFilter and cannot be null");
}
else
{
this.Keywords = keywords;
}
}
/// <summary>
/// Initializes a new instance of the <see cref="InputCollectionFilter" /> class.
/// </summary>
/// <param name="input">Collection of strings to filter (required).</param>
/// <param name="match">Match type (required) (default to MatchEnum.Any).</param>
/// <param name="keywords">Keywords (separate multiple values with commas) (required).</param>
public InputCollectionFilter(List <string> input = default(List <string>), MatchEnum match = MatchEnum.Any, string keywords = default(string))
{
// to ensure "input" is required (not null)
this.Input = input ?? throw new ArgumentNullException("input is a required property for InputCollectionFilter and cannot be null");
this.Match = match;
// to ensure "keywords" is required (not null)
this.Keywords = keywords ?? throw new ArgumentNullException("keywords is a required property for InputCollectionFilter and cannot be null");
}
private OverlapAnnotation(uint who, MatchEnum what, [CanBeNull] IInterval <uint> wow, BorderDistance where,
FailedReason why)
{
Who = who;
What = what;
Wow = wow;
Where = where;
Why = why;
}
public Comparison(GranularityEnum granularity, MatchEnum matchType, long newPosition, string newData, long oldPosition, string oldData)
{
_granularity = granularity;
_matchType = matchType;
_newPosition = newPosition;
_newData = newData;
_oldPosition = OldPosition;
_oldData = oldData;
}
private static void BuildChartTree(earley.State chart, ref List<string> tree, ref string s, MatchEnum? match = null)
{
if (hasSChanged)
{
foreach (var term in chart.termsRight.termsRight.StringListAfterDot())
if (term != earley.DOT && term == s)
tree.Add(term);
}
else
{
foreach (var term in chart.termsRight.termsRight)
if (term != earley.DOT && term == s)
tree.Add(term);
}
if (chart.termsLeft == "S")
{
tree.Add(chart.termsLeft);
collapse = true;
}
else
s = chart.termsLeft;
}
public static OverlapAnnotation Create(uint who, MatchEnum what, [CanBeNull] IInterval <uint> wow,
[NotNull] BorderDistance where, FailedReason why)
=> new OverlapAnnotation(who, what, wow, where, why);
