public BinEvidence GetBinEvidence(int numBins, int startPosition)
{
var binEvidence = new BinEvidence(_geminiSampleOptions.RefId.Value, _geminiOptions.CollectDepth,
numBins, _geminiOptions.AvoidLikelySnvs, _geminiOptions.MessySiteWidth, startPosition, trackDirectionalMess: _geminiOptions.SilenceDirectionalMessReads, trackMapqMess: _geminiOptions.SilenceMessyMapMessReads);
return(binEvidence);
}
public void GetBinId()
{
var binEvidence = new BinEvidence(1, true, 5000, false, 500, 123400);
Assert.Equal(0, binEvidence.GetBinId(123400));
Assert.Equal(0, binEvidence.GetBinId(123405));
Assert.Equal(0, binEvidence.GetBinId(123899));
Assert.Equal(1, binEvidence.GetBinId(123900));
Assert.Equal(1, binEvidence.GetBinId(123905));
// Position is out of range of the bins
// Still return the theoretical bin id, because it's handled elsewhere
Assert.Equal(5000, binEvidence.GetBinId(123400 + (500 * 5000) + 100));
Assert.Equal(5001, binEvidence.GetBinId(123400 + (500 * 5000) + 600));
}
public void AddAllHits()
{
var allHits = new uint[500];
var binEvidence = new BinEvidence(1, true, 500, false, 500, 123000);
var nonZeroBins = new Dictionary <int, int>();
binEvidence.AddAllHits(allHits);
CheckBins(500, nonZeroBins, (i) => binEvidence.GetAllHits(i));
allHits[25] = 18;
allHits[100] = 10;
nonZeroBins[25] = 18;
nonZeroBins[100] = 10;
binEvidence.AddAllHits(allHits);
CheckBins(500, nonZeroBins, (i) => binEvidence.GetAllHits(i));
// Test with AllHits not same size as BinEvidence
}
private static void CheckCorrectBinsIncremented(int numBins, Dictionary <int, int> messyHitNonZeroes, BinEvidence binEvidence,
Dictionary <int, int> indelHitNonZeroes, Dictionary <int, int> forwardMessNonZeroes, Dictionary <int, int> reverseMessNonZeroes,
Dictionary <int, int> mapqMessNonZeroes, Dictionary <int, int> singleMismatchNonZeroes, Dictionary <int, int> allHitsNonZeroes)
{
CheckBins(numBins, messyHitNonZeroes, (i) => binEvidence.GetMessyHit(i));
CheckBins(numBins, indelHitNonZeroes, (i) => binEvidence.GetIndelHit(i));
CheckBins(numBins, forwardMessNonZeroes, (i) => binEvidence.GetForwardMessyRegionHit(i));
CheckBins(numBins, reverseMessNonZeroes, (i) => binEvidence.GetReverseMessyRegionHit(i));
CheckBins(numBins, mapqMessNonZeroes, (i) => binEvidence.GetMapqMessyHit(i));
CheckBins(numBins, singleMismatchNonZeroes, (i) => binEvidence.GetSingleMismatchHit(i));
CheckBins(numBins, allHitsNonZeroes, (i) => binEvidence.GetAllHits(i));
}
public void AddMessEvidence()
{
var read1 = TestHelpers.CreateBamAlignment("ATCGATCG", 123405, 123505, 30, true);
var read2 = TestHelpers.CreateBamAlignment("ATCGATCG", 123505, 123405, 30, true);
var pair = new ReadPair(read1);
pair.AddAlignment(read2);
var pairResult = new PairResult(pair.GetAlignments(), pair);
var numBins = 5000;
var messyHitNonZeroes = new Dictionary <int, int>();
var indelHitNonZeroes = new Dictionary <int, int>();
var forwardMessNonZeroes = new Dictionary <int, int>();
var reverseMessNonZeroes = new Dictionary <int, int>();
var mapqMessNonZeroes = new Dictionary <int, int>();
var forwardMessNonZeroesNotUsed = new Dictionary <int, int>();
var reverseMessNonZeroesNotUsed = new Dictionary <int, int>();
var mapqMessNonZeroesNotUsed = new Dictionary <int, int>();
var singleMismatchNonZeroes = new Dictionary <int, int>();
var allHitsNonZeroes = new Dictionary <int, int>();
var binEvidence = new BinEvidence(1, true, numBins, false, 500, 123000, true, true);
var binEvidenceNoMapqMess = new BinEvidence(1, true, numBins, false, 500, 123000, true, false);
var binEvidenceNoDirectional = new BinEvidence(1, true, numBins, false, 500, 123000, false, true);
var binEvidenceNoDirectionalOrMapqMess = new BinEvidence(1, true, numBins, false, 500, 123000, false, false);
// Should add one piece of evidence for each alignment
// Read1 should be in bin 0, read2 in bin 1
// First, only messy
binEvidence.AddMessEvidence(true, pairResult, false, false, false, false, false);
allHitsNonZeroes[0] = 1;
allHitsNonZeroes[1] = 1;
messyHitNonZeroes[0] = 1;
messyHitNonZeroes[1] = 1;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(true, pairResult, false, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(true, pairResult, false, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(true, pairResult, false, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Add indel and mess evidence
binEvidence.AddMessEvidence(true, pairResult, true, false, false, false, false);
allHitsNonZeroes[0] = 2;
allHitsNonZeroes[1] = 2;
messyHitNonZeroes[0] = 2;
messyHitNonZeroes[1] = 2;
indelHitNonZeroes[0] = 1;
indelHitNonZeroes[1] = 1;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(true, pairResult, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(true, pairResult, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(true, pairResult, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Add forward mess (must also be called as mess - TODO perhaps change this)
binEvidence.AddMessEvidence(true, pairResult, false, false, true, false, false);
allHitsNonZeroes[0] = 3;
allHitsNonZeroes[1] = 3;
messyHitNonZeroes[0] = 3;
messyHitNonZeroes[1] = 3;
forwardMessNonZeroes[0] = 1;
forwardMessNonZeroes[1] = 1;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(true, pairResult, false, false, true, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(true, pairResult, false, false, true, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(true, pairResult, false, false, true, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Add reverse mess (must also be called as mess - TODO perhaps change this)
binEvidence.AddMessEvidence(true, pairResult, false, false, false, true, false);
allHitsNonZeroes[0] = 4;
allHitsNonZeroes[1] = 4;
messyHitNonZeroes[0] = 4;
messyHitNonZeroes[1] = 4;
reverseMessNonZeroes[0] = 1;
reverseMessNonZeroes[1] = 1;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(true, pairResult, false, false, false, true, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(true, pairResult, false, false, false, true, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(true, pairResult, false, false, false, true, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Add mapq mess (must also be called as mess - TODO perhaps change this)
binEvidence.AddMessEvidence(true, pairResult, false, false, false, false, true);
allHitsNonZeroes[0] = 5;
allHitsNonZeroes[1] = 5;
messyHitNonZeroes[0] = 5;
messyHitNonZeroes[1] = 5;
mapqMessNonZeroes[0] = 1;
mapqMessNonZeroes[1] = 1;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(true, pairResult, false, false, false, false, true);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(true, pairResult, false, false, false, false, true);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(true, pairResult, false, false, false, false, true);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Add indel only
binEvidence.AddMessEvidence(false, pairResult, true, false, false, false, false);
allHitsNonZeroes[0] = 6;
allHitsNonZeroes[1] = 6;
indelHitNonZeroes[0] = 2;
indelHitNonZeroes[1] = 2;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(false, pairResult, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(false, pairResult, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(false, pairResult, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
var read1_pair2 = TestHelpers.CreateBamAlignment("ATCGATCG", 125005, 126005, 30, true);
var read2_pair2 = TestHelpers.CreateBamAlignment("ATCGATCG", 126005, 125005, 30, true);
var pair2 = new ReadPair(read1_pair2);
pair2.AddAlignment(read2_pair2);
var pairResult2 = new PairResult(pair2.GetAlignments(), pair2);
// Add at different region
binEvidence.AddMessEvidence(false, pairResult2, true, false, false, false, false);
allHitsNonZeroes[4] = 1;
allHitsNonZeroes[6] = 1;
indelHitNonZeroes[4] = 1;
indelHitNonZeroes[6] = 1;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(false, pairResult2, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(false, pairResult2, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(false, pairResult2, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Test on diff chroms - mate on diff chrom shouldn't contribute
var read1_pair3 = TestHelpers.CreateBamAlignment("ATCGATCG", 125005, 126005, 30, true);
var read2_pair3 = TestHelpers.CreateBamAlignment("ATCGATCG", 126005, 125005, 30, true);
read2_pair3.RefID = 2;
read1_pair3.MateRefID = 2;
var pairSplitChrom = new ReadPair(read1_pair3);
pairSplitChrom.AddAlignment(read2_pair3);
var pairResultSplitChrom = new PairResult(pairSplitChrom.GetAlignments(), pairSplitChrom);
binEvidence.AddMessEvidence(false, pairResultSplitChrom, true, false, false, false, false);
allHitsNonZeroes[4] = 2;
indelHitNonZeroes[4] = 2;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(false, pairResultSplitChrom, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(false, pairResultSplitChrom, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(false, pairResultSplitChrom, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Read spans 2 bins (long read, or straddles two). Should increment in both.
var read1_pair4 = TestHelpers.CreateBamAlignment("ATCGATCG", 125005, 126495, 30, true);
var read2_pair4 = TestHelpers.CreateBamAlignment("ATCGATCG", 126495, 125005, 30, true);
var pairRead2Spans2Bins = new ReadPair(read1_pair4);
pairRead2Spans2Bins.AddAlignment(read2_pair4);
var pairResultRead2Spans2Bins = new PairResult(pairRead2Spans2Bins.GetAlignments(), pairRead2Spans2Bins);
binEvidence.AddMessEvidence(false, pairResultRead2Spans2Bins, true, false, false, false, false);
allHitsNonZeroes[4] = 3;
allHitsNonZeroes[6] = 2;
allHitsNonZeroes[7] = 1;
indelHitNonZeroes[4] = 3;
indelHitNonZeroes[6] = 2;
indelHitNonZeroes[7] = 1;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(false, pairResultRead2Spans2Bins, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(false, pairResultRead2Spans2Bins, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(false, pairResultRead2Spans2Bins, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Test mate goes outside of binEvidence region
var read1_pair5 = TestHelpers.CreateBamAlignment("ATCGATCG", 125005, 100026495, 30, true);
var read2_pair5 = TestHelpers.CreateBamAlignment("ATCGATCG", 100026495, 125005, 30, true);
var pairRead2PastRegion = new ReadPair(read1_pair5);
pairRead2PastRegion.AddAlignment(read2_pair5);
var pairResultRead2PastRegion = new PairResult(pairRead2PastRegion.GetAlignments(), pairRead2PastRegion);
binEvidence.AddMessEvidence(false, pairResultRead2PastRegion, true, false, false, false, false);
allHitsNonZeroes[4] = 4;
indelHitNonZeroes[4] = 4;
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidence, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using mapq mess
binEvidenceNoMapqMess.AddMessEvidence(false, pairResultRead2PastRegion, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoMapqMess, indelHitNonZeroes, forwardMessNonZeroes, reverseMessNonZeroes, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional
binEvidenceNoDirectional.AddMessEvidence(false, pairResultRead2PastRegion, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectional, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroes, singleMismatchNonZeroes, allHitsNonZeroes);
// Not using directional or mapq mess
binEvidenceNoDirectionalOrMapqMess.AddMessEvidence(false, pairResultRead2PastRegion, true, false, false, false, false);
CheckCorrectBinsIncremented(numBins, messyHitNonZeroes, binEvidenceNoDirectionalOrMapqMess, indelHitNonZeroes, forwardMessNonZeroesNotUsed, reverseMessNonZeroesNotUsed, mapqMessNonZeroesNotUsed, singleMismatchNonZeroes, allHitsNonZeroes);
}
public void GetAggregateRegionResults()
{
var geminiOptions = new GeminiOptions();
ChrReference chrReference = null;
var refIdMapping = new Dictionary <int, string>()
{
{ 1, "chr1" }
};
var bamRealignmentFactory = new BamRealignmentFactory(new GeminiOptions(),
new RealignmentAssessmentOptions(), new StitcherOptions(), new RealignmentOptions(), "out");
var geminiFactory = new GeminiFactory(geminiOptions, new IndelFilteringOptions());
var dataSourceFactoryMock = new Mock <IGeminiDataSourceFactory>();
var chromIndelSource = new Mock <IChromosomeIndelSource>();
//var indel = new KeyValuePair<HashableIndel, GenomeSnippet>();
chromIndelSource
.Setup(x => x.GetRelevantIndels(It.IsAny <int>(), It.IsAny <List <PreIndel> >(),
It.IsAny <List <HashableIndel> >(), It.IsAny <List <PreIndel> >(), It.IsAny <List <PreIndel> >())).Returns(new List <KeyValuePair <HashableIndel, GenomeSnippet> >()
{
//indel
});
dataSourceFactoryMock
.Setup(x => x.GetChromosomeIndelSource(It.IsAny <List <HashableIndel> >(),
It.IsAny <IGenomeSnippetSource>())).Returns(chromIndelSource.Object);
var dataSourceFactory = dataSourceFactoryMock.Object;
var masterIndelLookup = new ConcurrentDictionary <string, IndelEvidence>();
var masterOutcomesLookup = new ConcurrentDictionary <HashableIndel, int[]>();
var masterFinalIndels = new ConcurrentDictionary <HashableIndel, int>();
var categoriesForRealignment = new List <PairClassification>();
var progressTracker = new ConcurrentDictionary <string, int>();
var processor = new AggregateRegionProcessor(chrReference, refIdMapping, bamRealignmentFactory,
geminiOptions, geminiFactory, "chr1", dataSourceFactory, new RealignmentOptions()
{
CategoriesForSnowballing = new List <PairClassification>()
{
PairClassification.Disagree
}
},
masterIndelLookup, masterOutcomesLookup, masterFinalIndels, categoriesForRealignment, progressTracker);
var indelLookup = new ConcurrentDictionary <string, IndelEvidence>();
var binEvidence = new BinEvidence(1, true, 20, false, 500, 1000);
var edgeBinEvidence = new BinEvidence(1, true, 20, false, 500, 1000);
var edgeState = new EdgeState()
{
Name = "0-1000",
EdgeAlignments = new Dictionary <PairClassification, List <PairResult> >(),
BinEvidence = edgeBinEvidence,
EdgeIndels = new List <HashableIndel>(),
EffectiveMinPosition = 0
};
var pairResultLookup =
new ConcurrentDictionary <PairClassification, List <PairResult> >();
pairResultLookup.TryAdd(PairClassification.Disagree, new List <PairResult>()
{
TestHelpers.GetPairResult(10000),
TestHelpers.GetPairResult(10001),
TestHelpers.GetPairResult(10002),
TestHelpers.GetPairResult(19995)
});
pairResultLookup.TryAdd(PairClassification.SingleMismatchStitched, new List <PairResult>()
{
TestHelpers.GetPairResult(19995),
TestHelpers.GetPairResult(19995)
});
// Borderline case: the max position in the pair is >= EffectiveMaxPosition - 5000, even if one of the reads in the pair is not
var effectiveMax = 19999;
var r2BorderlinePos = effectiveMax - 5000 + 1;
var offset = 1;
var r1BorderlinePos = r2BorderlinePos - offset;
pairResultLookup.TryAdd(PairClassification.UnstitchForwardMessy, new List <PairResult>()
{
TestHelpers.GetPairResult(r1BorderlinePos, offset), // One is just over border
TestHelpers.GetPairResult(r1BorderlinePos, 0), // Both are within safe range
});
var regionData = new RegionDataForAggregation()
{
BinEvidence = binEvidence,
EdgeState = edgeState,
EffectiveMaxPosition = effectiveMax,
EffectiveMinPosition = 10000,
PairResultLookup = pairResultLookup
};
var regionResults = processor.GetAggregateRegionResults(indelLookup,
10000, 20000, false, regionData);
// New edge state should have the correct items carrying over
Assert.Equal("10000-20000", regionResults.EdgeState.Name);
Assert.Equal(14999, regionResults.EdgeState.EffectiveMinPosition);
Assert.Equal(4, regionResults.AlignmentsReadyToBeFlushed.Count); // The four that are solidly in-bounds should be flushable immediately
var edgeAlignmentsLookup = regionResults.EdgeState.EdgeAlignments;
Assert.Equal(1, edgeAlignmentsLookup[PairClassification.Disagree].Count);
Assert.Equal(2, edgeAlignmentsLookup[PairClassification.SingleMismatchStitched].Count);
Assert.Equal(1, edgeAlignmentsLookup[PairClassification.UnstitchForwardMessy].Count);
}
