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 void GetNm()
{
var snippetSource = new Mock <IGenomeSnippetSource>();
var genomeSnippet = new GenomeSnippet()
{
Chromosome = "chr1",
Sequence = "NNNNNAAAAATTTTTGGGGGCCCCC",
StartPosition = 94 // 0 based
};
snippetSource.Setup(x => x.GetGenomeSnippet(It.IsAny <int>())).Returns(genomeSnippet);
var nmCalculator = new NmCalculator(snippetSource.Object);
// Positions passed to CreateBamAlignment are one based bc it adjusts by one in the helper
var alignment = TestHelpers.CreateBamAlignment("AAAAA", 100, 0, 30, true);
Assert.Equal(0, nmCalculator.GetNm(alignment));
alignment = TestHelpers.CreateBamAlignment("AATAA", 100, 0, 30, true);
Assert.Equal(1, nmCalculator.GetNm(alignment));
alignment = TestHelpers.CreateBamAlignment("AGTGT", 100, 0, 30, true);
Assert.Equal(4, nmCalculator.GetNm(alignment));
alignment = TestHelpers.CreateBamAlignment("AGTGT", 100, 0, 30, true, cigar: new CigarAlignment("1M4I"));
Assert.Equal(4, nmCalculator.GetNm(alignment));
alignment = TestHelpers.CreateBamAlignment("ATTTT", 100, 0, 30, true, cigar: new CigarAlignment("1M4D4M"));
Assert.Equal(4, nmCalculator.GetNm(alignment));
alignment = TestHelpers.CreateBamAlignment("ACCCC", 100, 0, 30, true, cigar: new CigarAlignment("1M4D4M"));
Assert.Equal(8, nmCalculator.GetNm(alignment));
alignment = TestHelpers.CreateBamAlignment("GAAAA", 100, 0, 30, true);
Assert.Equal(1, nmCalculator.GetNm(alignment));
alignment = TestHelpers.CreateBamAlignment("AATAA", 100, 0, 30, true, cigar: new CigarAlignment("2M3S"));
Assert.Equal(0, nmCalculator.GetNm(alignment));
}
private List <BamAlignment> ProcessCategory(
List <PairClassification> categoriesForRealignment, IChromosomeIndelSource indelSource,
bool shouldRealignAtAll, Dictionary <HashableIndel, int[]> outcomesLookup, ref int numSkippedDueToSites,
ref int numKept, ref int numRealigned, ref int numSilenced,
List <PairResult> pairResults, PairClassification classification, IBinEvidence binEvidence,
ConcurrentDictionary <string, int> progressTracker, BinConclusions binConclusions, UsableBins usableBins, int startPosition, int endPosition)
{
var allAlignments = new List <BamAlignment>();
var isHighLikelihoodForRealign = false;
if (_geminiOptions.ForceHighLikelihoodRealigners)
{
var highLikelihoodCategories = new List <PairClassification>()
{
PairClassification.Disagree,
PairClassification.MessyStitched,
PairClassification.MessySplit,
PairClassification.UnstitchMessy,
PairClassification.UnstitchIndel
};
isHighLikelihoodForRealign = highLikelihoodCategories.Contains(classification);
}
int alignmentsCount = 0;
var doRealign = false;
ReadPairRealignerAndCombiner realignHandler = null;
var alreadyStitched = ClassificationIsStitched(classification);
var doStitch = !_geminiOptions.SkipStitching && TypeClassifier.ClassificationIsStitchable(classification);
var categoryIsRealignable = categoriesForRealignment.Contains(classification);
if (categoryIsRealignable || doStitch)
{
doRealign = true;
realignHandler = _bamRealignmentFactory.GetRealignPairHandler(doStitch,
alreadyStitched,
_realignmentOptions.PairAwareEverything ||
ClassificationIsPairAwareRealignable(classification),
_refIdMapping,
new ReadStatusCounter(), false, indelSource, _chrom, new Dictionary <string, IndelEvidence>(),
ClassificationHasIndels(classification), outcomesLookup
, SkipRestitchIfUnchanged(classification));
}
using (var snippetSource = _dataSourceFactory.CreateGenomeSnippetSource(_chrom, _chrReference))
using (var singleSnippetSource = new ReusableSnippetSource(snippetSource))
{
var nmCalculator = new NmCalculator(singleSnippetSource);
var classificationString = classification.ToString();
foreach (var pairResult in pairResults)
{
int toSilence = 0;
IEnumerable <BamAlignment> alignments;
if (!doRealign)
{
alignments = pairResult.Alignments;
}
else
{
bool doRealignPair =
shouldRealignAtAll && (isHighLikelihoodForRealign ||
(categoryIsRealignable &&
(usableBins.IsPositionUsable(pairResult.ReadPair.MinPosition) ||
usableBins.IsPositionUsable(pairResult.ReadPair.MaxPosition))));
if (!doRealignPair)
{
numSkippedDueToSites++;
}
else
{
numKept++;
}
toSilence = ReadsToSilence(classification, binConclusions, pairResult);
if (toSilence > 0)
{
numSilenced++;
}
alignments = realignHandler.ExtractReads(pairResult, nmCalculator, doRealignPair, toSilence);
if (pairResult.ReadPair.Realigned || pairResult.ReadPair.RealignedR1 ||
pairResult.ReadPair.RealignedR2)
{
numRealigned++;
}
}
var silencedR1 = (toSilence == 1 || toSilence == 3) && !pairResult.ReadPair.RealignedR1;
var silencedR2 = (toSilence == 2 || toSilence == 3) && !pairResult.ReadPair.RealignedR2;
var readTreatment = ReadTreatment(silencedR1, silencedR2, pairResult);
progressTracker.AddOrUpdate(classificationString + ":" + readTreatment, 1,
(x, currentCount) => { return(currentCount + 1); });
var alignmentsList = alignments.ToList();
foreach (var bamAlignment in alignmentsList)
{
if (_geminiOptions.LightDebug)
{
AddMdTagCountsTags(bamAlignment, pairResult);
}
bamAlignment.ReplaceOrAddStringTag("XT", readTreatment);
bamAlignment.ReplaceOrAddStringTag("XP", classificationString);
}
alignmentsCount += alignmentsList.Count();
allAlignments.AddRange(alignmentsList);
}
}
if (realignHandler != null)
{
realignHandler.Finish();
}
pairResults.Clear();
return(allAlignments);
}
