public void AgeIsCorrectlyPrinted()
{
string description = new Genome(age: 3).ToString();
Assert.True(description.Contains("Age: 3"), $"Genome's age is not printed. Print was: {description}.");
}
/// <summary>
/// Determines the matching segments shared by this and the specified Genome.
/// </summary>
/// <param name="other">The other Genome to compare.</param>
/// <param name="minSnpCount">The minimum number of contiguous matching Snp allele values to be considered a valid match.</param>
/// <param name="minCm">The minimum length of a segment in centiMorgans to be considered a valid match.</param>
/// <param name="minStitchCm">The minimum length of each of two segments that may be stitched together when separated by a single mismatch.</param>
/// <param name="minStitchSnpCount">The minimum number of contiguous matching SNP allele values in each of two segments that may be
/// stitched together when separated by a single mismatch.</param>
/// <param name="onlyFull">Specifies whether </param>
/// <returns>An IList of SegmentMatch structs describing the matching segments that were identified.</returns>
public IList<SegmentMatch> MatchingSegments(Genome other, int minSnpCount, double minCm,
int minStitchSnpCount, double minStitchCm, bool onlyFull) {
var snps = this.GetSnps();
var result = new List<SegmentMatch>();
int matchCount = 0;
int hoHoSnpCount = 0;
var prevChr = -1;
Snp startSnp, endSnp;
startSnp = endSnp = null;
int snpCount = 0;
int genomeSnpCount = snps.Count;
bool canJoinWithPrevious = false;
foreach (var snp in snps) {
snpCount++;
byte alleles = this.genotypes[snp];
bool hoho = alleles.IsHomozygous();
alleles &= Allele.AllAlleles;
if ((alleles != Allele.AT) && ((alleles & Allele.T) != 0)) alleles ^= Allele.AT;
if ((alleles != Allele.CG) && ((alleles & Allele.G) != 0)) alleles ^= Allele.CG;
byte otherAlleles = Allele.Null;
if (other.Contains(snp)) otherAlleles = other[snp];
hoho &= otherAlleles.IsHomozygous();
otherAlleles &= Allele.AllAlleles;
if ((otherAlleles != Allele.AT) && ((otherAlleles & Allele.T) != 0)) otherAlleles ^= Allele.AT;
if ((otherAlleles != Allele.CG) && ((otherAlleles & Allele.G) != 0)) otherAlleles ^= Allele.CG;
bool haveNull = ((alleles == Allele.Null) || (otherAlleles == Allele.Null));
hoho &= !haveNull;
bool sameChromosome = (snp.Chromosome == prevChr);
bool buildingMatch = (matchCount > 0);
bool haveMatch = (haveNull && buildingMatch && sameChromosome) || ((alleles == otherAlleles) && !haveNull);
if (!onlyFull) haveMatch = haveMatch || ((alleles & otherAlleles) != 0);
if (buildingMatch) {
if (haveMatch && sameChromosome && (snpCount != genomeSnpCount)) {
endSnp = snp;
if (!haveNull) {
matchCount++;
if (hoho) hoHoSnpCount++;
}
} else {
if ((matchCount >= minStitchSnpCount) && (endSnp.cM - startSnp.cM >= minStitchCm)) {
// matching segment is big enough to keep
if (canJoinWithPrevious) {
var lastMatch = result[result.Count - 1];
result[result.Count - 1] = new SegmentMatch(lastMatch.StartSnp, endSnp,
lastMatch.SnpCount + matchCount, lastMatch.HoHoSnpCount + hoHoSnpCount,
lastMatch.HalvesMatched);
} else {
result.Add(new SegmentMatch(startSnp, endSnp, matchCount, hoHoSnpCount, onlyFull ? 2 : 1));
}
canJoinWithPrevious = sameChromosome;
} else {
if (!haveNull) canJoinWithPrevious = false;
}
if (haveMatch) { //we're on next chromosome and it starts with a match
startSnp = endSnp = snp;
matchCount = 1;
if (hoho) hoHoSnpCount = 1;
} else {
startSnp = endSnp = null;
matchCount = 0;
hoHoSnpCount = 0;
}
}
} else { // !buildingMatch
if (haveMatch) {
startSnp = endSnp = snp;
matchCount = 1;
if (hoho) hoHoSnpCount = 1;
} else {
if (!haveNull) canJoinWithPrevious = false;
}
}
prevChr = snp.Chromosome;
}
List<SegmentMatch> filteredResult = new List<SegmentMatch>();
if ((minSnpCount != minStitchSnpCount) || (minCm != minStitchCm)) {
foreach (var match in result) {
if ((match.SnpCount >= minSnpCount) && (match.CmLength >= minCm)) {
filteredResult.Add(match);
}
}
return filteredResult;
} else {
return result;
}
}