public static void AddEvidence(PairResult pairResult, int siteWidth, int regionStart,
ConcurrentDictionary <int, uint> allHits, ConcurrentDictionary <int, uint> probableTrueSnvRegionsLookup,
bool isSingleMismatch, int numBins, int refId)
{
foreach (var aln in pairResult.Alignments)
{
if (aln.RefID != refId)
{
continue;
}
var lastBinSpannedByRead = (aln.EndPosition - regionStart) / siteWidth;
var firstBin = (aln.Position - regionStart) / siteWidth;
for (int i = firstBin; i <= Math.Min(lastBinSpannedByRead, numBins - 1); i++)
{
allHits[i]++;
if (isSingleMismatch)
{
probableTrueSnvRegionsLookup[i]++;
}
}
}
}
public int Find(IRawFile reader, int scan)
{
PairResult pr;
if (!map.TryGetValue(reader, out pr) || !reader.FileName.Equals(pr.FileName))
{
pr = new PairResult()
{
FileName = reader.FileName,
ScanMap = builder.GetScanLevels(reader).ToDictionary(m => m.Scan)
};
map[reader] = pr;
}
ScanLevel level;
if (pr.ScanMap.TryGetValue(scan, out level))
{
if (level.Parent != null)
{
return(level.Parent.Scan);
}
}
return(0);
}
public override PairResult[] GetValueOutput()
{
PairResult[] res = new PairResult[3];
res[0] = new PairResult() { Title = TAG_TITLE + this.Name, Value = Tag };
res[1] = new PairResult() { Title = LENGTH_TITLE + this.Name, Value = Length.ToString("X2")};
res[2] = new PairResult() { Title = VALUE_TITLE+ this.Name, Value = Value};
return res;
}
private static void AddMdTagCountsTags(BamAlignment bamAlignment, PairResult pairResult)
{
if (pairResult.md1.IsSet)
{
bamAlignment.ReplaceOrAddStringTag("XM",
$"A: {pairResult.md1.A},{pairResult.md2.A}; T: {pairResult.md1.T},{pairResult.md2.T}; C: {pairResult.md1.C},{pairResult.md2.C}; G: {pairResult.md1.G},{pairResult.md2.G}; subA: {pairResult.md1.SubA},{pairResult.md2.SubA}; subT: {pairResult.md1.SubT},{pairResult.md2.SubT}; subC: {pairResult.md1.SubC},{pairResult.md2.SubC}; subG: {pairResult.md1.SubG},{pairResult.md2.SubG}; subN: {pairResult.md1.SubN},{pairResult.md2.SubN}; maxRun: {pairResult.md1.RunLength},{pairResult.md2.RunLength}; numRuns: {pairResult.md1.NumInRuns},{pairResult.md2.NumInRuns}");
}
else
{
bamAlignment.ReplaceOrAddStringTag("XM", $"Not set");
}
}
public List <PairResult> GetPairList()
{
var result = new List <PairResult>();
var pairs = EnumUtil.GetValues <FiatCurrency>();
foreach (var pair in pairs)
{
var pairResult = new PairResult()
{
Id = (int)pair,
Symbol = pair.ToString()
};
result.Add(pairResult);
}
return(result);
}
private static List <BamAlignment> ExtractReadsFromRealignerAndCombiner(PairResult pair, string refSeq,
int refSeqOffset, List <PreIndel> preIndels, bool hasExistingIndels = false)
{
var stitchedPairHandler =
new PairHandler(new Dictionary <int, string>()
{
{ 1, "chr1" }
}, new BasicStitcher(0), tryStitch: true);
var snippetSource = new Mock <IGenomeSnippetSource>();
var genomeSnippet = new GenomeSnippet()
{
Chromosome = "chr1",
Sequence = new string('A', refSeqOffset) + refSeq + new string('T', 1000),
StartPosition = 0
};
snippetSource.Setup(x => x.GetGenomeSnippet(It.IsAny <int>())).Returns(genomeSnippet);
var mockStatusHandler = new Mock <IStatusHandler>();
var comparer = new GemBasicAlignmentComparer(false, false);
var readRealigner = new GeminiReadRealigner(comparer, remaskSoftclips: false,
keepProbeSoftclips: false, keepBothSideSoftclips: false,
trackActualMismatches: false, checkSoftclipsForMismatches: true,
debug: false, maskNsOnly: false, maskPartialInsertion: false,
minimumUnanchoredInsertionLength: 1,
minInsertionSizeToAllowMismatchingBases: 4,
maxProportionInsertSequenceMismatch: 0.2); // TODO fix // TODO figure out what I was saying to fix here...
var filterer = new Mock <IRegionFilterer>();
filterer.Setup(x => x.AnyIndelsNearby(It.IsAny <int>())).Returns(true);
var indels = preIndels.Select(x => HashableIndelSource.GetHashableIndel(genomeSnippet, x, 0, false)).ToList();
var indelSource = new ChromosomeIndelSource(indels, snippetSource.Object);
var realignmentEvaluator = new RealignmentEvaluator(indelSource, mockStatusHandler.Object, readRealigner,
new RealignmentJudger(comparer), "chr1", false, true, true, true, filterer.Object, false);
var combiner = new ReadPairRealignerAndCombiner(new NonSnowballEvidenceCollector(),
new PostRealignmentStitcher(stitchedPairHandler, new DebugStatusHandler(new ReadStatusCounter())),
realignmentEvaluator, new PairSpecificIndelFinder(), "chr1", false, hasExistingIndels: hasExistingIndels);
var nmCalc = new NmCalculator(snippetSource.Object);
var result = combiner.ExtractReads(pair, nmCalc);
return(result);
}
public static PairResult GetPairResult(int position, int offset = 0,
string r1Cigar = "5M1I5M", string r2Cigar = "5M1I5M",
PairClassification classification = PairClassification.Unknown,
int numMismatchesInSingleton = 0, int softclipLength = 0, bool hasIndels = false, bool isReputableIndelContaining = false)
{
//var read1 = TestHelpers.CreateBamAlignment("ATCGATCG", 125005, 126005, 30, true);
//var read2 = TestHelpers.CreateBamAlignment("ATCGATCG", 126005, 125005, 30, true);
//var pair2 = new ReadPair(read1);
//pair2.AddAlignment(read2);
var readPair1 = TestHelpers.GetPair(r1Cigar, r2Cigar, read2Offset: offset, read1Position: position);
var pairResult2 = new PairResult(readPair1.GetAlignments(), readPair1, classification: classification, numMismatchesInSingleton: numMismatchesInSingleton, softclipLengthForIndelRead: softclipLength, hasIndels: hasIndels);
pairResult2.IsReputableIndelContaining = isReputableIndelContaining;
return(pairResult2);
}
public IEnumerable <PairResult> GetPairsMatch([FromUri] int id)
{
FishingMatch fishingMatch = Get(id);
var pairResults = new List <PairResult>();
if (!fishingMatch.IsPairs)
{
return(pairResults);
}
foreach (MatchEntry matchEntry in fishingMatch.MatchEntries)
{
bool toAdd = !pairResults.Any(pair => pair.Peg1 == matchEntry.Peg || pair.Peg2 == matchEntry.Peg);
if (!toAdd)
{
continue;
}
var matchEntryPair = new List <MatchEntry> {
matchEntry
};
MatchEntry pairedMatchEntry = fishingMatch.MatchEntries.Single(me => me.PairedWithPeg == matchEntry.Peg);
matchEntryPair.Add(pairedMatchEntry);
var pairResult = new PairResult
{
Angler1 = matchEntryPair[0].AnglerName,
Angler2 = matchEntryPair[1].AnglerName,
Peg1 = matchEntryPair[0].Peg,
Peg2 = matchEntryPair[1].Peg,
Weight = matchEntryPair[0].Weight + matchEntryPair[1].Weight
};
if (pairResult.Peg1 == pairResult.Peg2)
{
pairResult.Peg2 = null;
pairResult.Angler2 = "(weight doubled)";
}
pairResults.Add(pairResult);
}
return(pairResults.OrderByDescending(result => result.Weight));
}
public override PairResult[] GetValueOutput()
{
PairResult[] res = new PairResult[3];
res[0] = new PairResult()
{
Title = TAG_TITLE + this.Name, Value = Tag
};
res[1] = new PairResult()
{
Title = LENGTH_TITLE + this.Name, Value = Length.ToString("X2")
};
res[2] = new PairResult()
{
Title = VALUE_TITLE + this.Name, Value = Value
};
return(res);
}
private static string ReadTreatment(bool silencedR1, bool silencedR2, PairResult pairResult)
{
var silencedStatus = silencedR1 || silencedR2
? ($"_Silenced{(silencedR1 ? "R1" : "")}{(silencedR2 ? "R2" : "")}")
: "";
var readTreatment =
(pairResult.ReadPair.RealignedR1 ? "R1Realigned" :
pairResult.R1Confirmed ? "R1Confirmed" : "R1Untouched") + "_" +
(pairResult.ReadPair.RealignedR2 ? "R2Realigned" :
pairResult.R2Confirmed ? "R2Confirmed" : "R2Untouched") + "_" +
(pairResult.ReadPair.Stitched ? "Stitched" :
pairResult.ReadPair.BadRestitch ? "BadRestitch" :
pairResult.ReadPair.FailForOtherReason ? "FailStitch" :
pairResult.ReadPair.Disagree ? "Disagree" :
pairResult.TriedStitching ? "GenericFailStitch" : "Unstitch") + silencedStatus;
return(readTreatment);
}
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 List <BamAlignment> ExtractReads(PairResult pairResult, INmCalculator nmCalculator, bool doRealign = true, int readsToSilence = 0)
{
var pair = pairResult.ReadPair;
if (pair.PairStatus == PairStatus.LeaveUntouched)
{
return(pair.GetAlignments().ToList());
}
var reads = new List <BamAlignment>();
// TODO clean this up, should really not have two layers (pair result and readpair) here
if (pairResult.ReadPair.Stitched)
{
const bool recalculateNm = true; // Always recalculate NM for stitched reads
// TODO more explicitly assume/check that there is actually only one here
foreach (var alignment in pairResult.Alignments)
{
if (doRealign)
{
var finalReadR1 = RealignSingleAlignment(alignment, out var realignedR1);
pair.RealignedR1 = realignedR1;
SilenceReads(finalReadR1, null, readsToSilence, realignedR1, false);
pair.StitchedNm = UpdateAndAddAlignment(finalReadR1, false, null, reads, nmCalculator, recalculateNm);
}
else
{
SilenceReads(alignment, null, readsToSilence, false, false);
pair.StitchedNm = UpdateAndAddAlignment(alignment, false, null, reads, nmCalculator, recalculateNm);
}
}
return(reads);
}
if (pair.IsComplete(false) && (pair.PairStatus == PairStatus.Paired || pair.PairStatus == PairStatus.OffTarget))
{
var realignedR1 = false;
var realignedR2 = false;
var forcedSoftclipR1 = false;
var forcedSoftclipR2 = false;
var sketchy = false;
var origRead1 = pair.Read1;
var origRead2 = pair.Read2;
int? r1Nm = pair.Read1.GetIntTag("NM");
int? r2Nm = pair.Read2.GetIntTag("NM");
List <PreIndel> pairIndels = null;
if (pair.PairStatus == PairStatus.Paired)
{
if (doRealign)
{
List <PreIndel> r1Indels = _hasExistingIndels && pairResult.R1Nm <= 2
? pairResult.OriginalIndelsR1 ?? _indelTargetFinder.FindIndels(origRead1, _chromosome)
: _emptyList;
List <PreIndel> r2Indels = _hasExistingIndels && pairResult.R2Nm <= 2
? pairResult.OriginalIndelsR2 ?? _indelTargetFinder.FindIndels(origRead2, _chromosome)
: _emptyList;
if (_pairAware && _hasExistingIndels && (r1Indels.Any() || r2Indels.Any()))
{
pairIndels = _finder.GetPairSpecificIndels(pair, r1Indels, r2Indels, ref r1Nm, ref r2Nm);
}
var confirmedAccepted = new List <HashableIndel>();
bool confirmedR1;
bool confirmedR2;
// TODO should we pay attention to whether one already has an indel and one doesn't, and realign/confirm the one that does, or that has the better one, first?
var try1Read1 = _evaluator.GetFinalAlignment(origRead1,
out realignedR1, out forcedSoftclipR1, out confirmedR1, out sketchy, selectedIndels: pairIndels,
existingIndels: r1Indels, confirmedAccepteds: confirmedAccepted, mateIndels: r2Indels);
pair.Read1 = try1Read1;
if ((realignedR1 || confirmedR1) && confirmedAccepted.Any())
{
pair.Read2 = _evaluator.GetFinalAlignment(origRead2,
out realignedR2, out forcedSoftclipR2, out confirmedR2, out sketchy, selectedIndels: pairIndels,
existingIndels: r2Indels, confirmedAccepteds: confirmedAccepted);
}
else
{
confirmedAccepted.Clear();
var try1Read2 = _evaluator.GetFinalAlignment(origRead2,
out realignedR2, out forcedSoftclipR2, out confirmedR2, out sketchy, selectedIndels: pairIndels,
existingIndels: r2Indels, confirmedAccepteds: confirmedAccepted, mateIndels: r1Indels);
pair.Read2 = try1Read2;
if ((realignedR2 || confirmedR2) && confirmedAccepted.Any())
{
pair.Read1 = _evaluator.GetFinalAlignment(origRead1,
out realignedR1, out forcedSoftclipR1, out confirmedR1, out sketchy, selectedIndels: pairIndels,
existingIndels: r1Indels, confirmedAccepteds: confirmedAccepted);
}
}
pairResult.R1Confirmed = confirmedR1;
pairResult.R2Confirmed = confirmedR2;
}
if (realignedR1 || realignedR2)
{
pair.Realigned = true;
}
}
pair.RealignedR1 = realignedR1;
pair.RealignedR2 = realignedR2;
// Silence realigned pair if needed
SilenceReads(pair.Read1, pair.Read2, readsToSilence, realignedR1, realignedR2);
// Silence original reads in case needed
SilenceReads(origRead1, origRead2, readsToSilence, false, false);
if (_allowedToStitch && !(forcedSoftclipR1 || forcedSoftclipR2) && (!_skipRestitchIfNothingChanged || (realignedR1 || realignedR2)))
{
reads = _restitcher.GetRestitchedReads(pair, origRead1, origRead2, r1Nm, r2Nm, pairIndels != null, nmCalculator,
realignedR1 || realignedR2 || (r1Nm + r2Nm > 0), sketchy);
var isStitched = reads.Count == 1;
pair.Stitched = isStitched;
pairResult.TriedStitching = true;
if (!isStitched)
{
reads.Clear();
// TODO looks like we are passing through EC twice - here and in the below foreach
HandleUnstitchedReads(pair, reads, realignedR1, realignedR2, nmCalculator);
}
foreach (var bamAlignment in reads)
{
_evidenceCollector.CollectEvidence(bamAlignment, true, isStitched, _chromosome);
}
}
else
{
HandleUnstitchedReads(pair, reads, realignedR1, realignedR2, nmCalculator);
}
}
else
{
if (doRealign)
{
var finalReadR1 = RealignSingleAlignment(pair.Read1, out var realignedR1);
var finalReadR2 = RealignSingleAlignment(pair.Read2, out var realignedR2);
pair.RealignedR1 = realignedR1;
pair.RealignedR2 = realignedR2;
if (realignedR1 || realignedR2)
{
pair.Realigned = true;
}
SilenceReads(finalReadR1, finalReadR2, readsToSilence, realignedR1, realignedR2);
pair.Nm1 = UpdateAndAddAlignment(finalReadR1, realignedR2, finalReadR2, reads, nmCalculator, realignedR1);
pair.Nm2 = UpdateAndAddAlignment(finalReadR2, realignedR1, finalReadR1, reads, nmCalculator, realignedR2);
}
else
{
SilenceReads(pair.Read1, pair.Read2, readsToSilence, false, false);
pair.Nm1 = UpdateAndAddAlignment(pair.Read1, false, pair.Read2, reads, nmCalculator, false);
pair.Nm2 = UpdateAndAddAlignment(pair.Read2, false, pair.Read1, reads, nmCalculator, false);
}
}
return(reads);
}
public void AddMessEvidence(bool isMessy, PairResult pairResult, bool isIndel, bool isSingleMismatch, bool isForwardOnlyMessy, bool isReverseOnlyMessy, bool isMapqMessy)
{
if (!_collectDepth && !isMessy && !isIndel && !isForwardOnlyMessy && !isMapqMessy && !isReverseOnlyMessy && !isSingleMismatch)
{
return;
}
foreach (var aln in pairResult.Alignments)
{
if (aln.RefID != _refId)
{
continue;
}
var lastBinSpannedByRead = GetBinId(aln.EndPosition);
var firstBin = GetBinId(aln.Position);
if (lastBinSpannedByRead + 1 > NumBins - 1)
{
Console.WriteLine("LAST BIN SPANNED IS GREATER THAN ALLHITS!!!");
}
for (int i = firstBin; i <= Math.Min(lastBinSpannedByRead, NumBins - 1); i++)
{
try
{
AllHits.AddHit(i);
if (isMessy)
{
AddMessyHit(i);
if (isForwardOnlyMessy)
{
_fwdOnlyMessyHits.AddHit(i);
}
else if (isReverseOnlyMessy)
{
_revOnlyMessyHits.AddHit(i);
}
else if (isMapqMessy)
{
_mapqMessyHits.AddHit(i);
}
}
if (isIndel)
{
AddIndelHit(i);
}
if (isSingleMismatch)
{
AddSingleMismatchHit(i);
}
}
catch (Exception e)
{
Console.WriteLine($"FAILED ON {i} ({aln.Position}, {_regionStart})..." + e.Message);
throw new Exception($"FAILED ON {i} ({aln.Position}, {_regionStart})", e);
}
}
}
}
private int ReadsToSilence(PairClassification classification, BinConclusions binEvidence, PairResult pairResult)
{
if (_geminiOptions.SilenceSuspiciousMdReads && classification == PairClassification.UnstitchMessySuspiciousMd)
{
return(3);
}
var isForwardMessy = IsForwardMessy(classification);
var isReverseMessy = IsReverseMessy(classification);
var isSuspiciousMapping = IsSuspiciousMapping(classification);
if (!isForwardMessy && !isReverseMessy && !isSuspiciousMapping)
{
return(0);
}
var silenced = 0;
var doSilenceFwd = false;
var doSilenceRev = false;
var r1IsReverse = pairResult.ReadPair.Read1.IsReverseStrand();
// This assumes that there is exactly one forward and one reverse read.
var fwdRead = r1IsReverse ? pairResult.ReadPair.Read2 : pairResult.ReadPair.Read1;
var revRead = r1IsReverse ? pairResult.ReadPair.Read1 : pairResult.ReadPair.Read2;
if (isForwardMessy)
{
var binId = binEvidence.GetBinId(fwdRead.Position);
doSilenceFwd = binEvidence.GetFwdMessyStatus(binId) || binEvidence.GetMapqMessyStatus(binId);
}
else if (isReverseMessy)
{
var binId = binEvidence.GetBinId(revRead.Position);
doSilenceRev = binEvidence.GetRevMessyStatus(binId) || binEvidence.GetMapqMessyStatus(binId);
}
else if (isSuspiciousMapping)
{
var binId = binEvidence.GetBinId(revRead.Position);
var isMapqMessy = binEvidence.GetMapqMessyStatus(binId);
doSilenceFwd = isMapqMessy;
doSilenceRev = isMapqMessy;
}
if (doSilenceFwd)
{
silenced = r1IsReverse ? 2 : 1;
}
if (doSilenceRev)
{
silenced = r1IsReverse ? 1 : 2;
}
if (doSilenceFwd && doSilenceRev)
{
silenced = 3;
}
return(silenced);
}
