private static bool CanBeSame(AlleleBlock alleleBlock, AlleleBlock seedBlock, out int missingBasesBefore, out int missingBasesAfter)
{
missingBasesBefore = 0;
missingBasesAfter = 0;
int endIndexSeedBlock = seedBlock.PositionIndex + seedBlock.AlleleIndexes.Length - 1;
int endIndexThisBlock = alleleBlock.PositionIndex + alleleBlock.AlleleIndexes.Length - 1;
if (endIndexThisBlock > endIndexSeedBlock)
{
return(false);
}
missingBasesBefore = alleleBlock.PositionIndex - seedBlock.PositionIndex;
if (alleleBlock.NumRefPositionsBefore < missingBasesBefore)
{
return(false);
}
missingBasesAfter = endIndexSeedBlock - endIndexThisBlock;
if (alleleBlock.NumRefPositionsAfter < missingBasesAfter)
{
return(false);
}
for (var i = 0; i < missingBasesBefore; i++)
{
if (seedBlock.AlleleIndexes[i] != 0)
{
return(false);
}
}
for (var i = 0; i < alleleBlock.AlleleIndexes.Length; i++)
{
if (alleleBlock.AlleleIndexes[i] != seedBlock.AlleleIndexes[i + missingBasesBefore])
{
return(false);
}
}
for (int i = missingBasesBefore + alleleBlock.AlleleIndexes.Length;
i < seedBlock.AlleleIndexes.Length;
i++)
{
if (seedBlock.AlleleIndexes[i] != 0)
{
return(false);
}
}
return(true);
}
internal static AlleleBlock ExtendAlleleBlock(AlleleBlock alleleBlock, int extendBefore, int extendAfter)
{
if (extendBefore > alleleBlock.NumRefPositionsBefore)
{
throw new ArgumentOutOfRangeException($"Can't extend an allele block with {alleleBlock.NumRefPositionsBefore} trimmed leading reference positions by adding {extendBefore} reference positions before it");
}
if (extendAfter > alleleBlock.NumRefPositionsAfter)
{
throw new ArgumentOutOfRangeException($"Can't extend an allele block with {alleleBlock.NumRefPositionsAfter} trimmed trailing reference positions by adding {extendAfter} reference positions after it");
}
int lengthOldAlleleIndexes = alleleBlock.AlleleIndexes.Length;
var newAlleleIndexes = new int[extendBefore + lengthOldAlleleIndexes + extendAfter];
Array.Copy(alleleBlock.AlleleIndexes, 0, newAlleleIndexes, extendBefore, lengthOldAlleleIndexes);
return(new AlleleBlock(alleleBlock.PositionIndex - extendBefore, newAlleleIndexes, -1, -1));
}
public static PositionSet CreatePositionSet(List <ISimplePosition> simpleSimplePositions, List <int> functionBlockRanges)
{
var positionSet = new PositionSet(simpleSimplePositions, functionBlockRanges);
positionSet.AlleleSet = GenerateAlleleSet(positionSet);
positionSet._allelesWithUnsupportedTypes = GetAllelesWithUnsupportedTypes(positionSet);
positionSet._sampleInfo = GetSampleInfo(positionSet);
var phaseSetAndGqIndexes = positionSet.GetSampleTagIndexes(new[] { "GT", "PS", "GQ" });
positionSet.GtInfo = TagInfo <Genotype> .GetTagInfo(positionSet._sampleInfo, phaseSetAndGqIndexes[0], ExtractSampleValue, Genotype.GetGenotype);
positionSet.PsInfo = TagInfo <string> .GetTagInfo(positionSet._sampleInfo, phaseSetAndGqIndexes[1], ExtractSampleValue, x => x);
positionSet.GqInfo = TagInfo <string> .GetTagInfo(positionSet._sampleInfo, phaseSetAndGqIndexes[2], ExtractSampleValue, x => x);
var genotypeToSampleIndex = GetGenotypeToSampleIndex(positionSet);
var alleleBlockToSampleHaplotype = AlleleBlock.GetAlleleBlockToSampleHaplotype(genotypeToSampleIndex, positionSet._allelesWithUnsupportedTypes, positionSet.AlleleSet.Starts, positionSet.FunctionBlockRanges, out var alleleBlockGraph);
positionSet.AlleleBlockToSampleHaplotype = AlleleBlockMerger.Merge(alleleBlockToSampleHaplotype, alleleBlockGraph);
return(positionSet);
}
private static bool SeedOutOfRange(AlleleBlock alleleBlock, AlleleBlock seedBlock) => seedBlock.PositionIndex + seedBlock.AlleleIndexes.Length - 1 < alleleBlock.PositionIndex;
