public void GetGenomeSnippet()
{
var genome = new Mock <IGenome>();
genome.Setup(x => x.GetChrReference("chr1"))
.Returns(new ChrReference()
{
Sequence = new string('A', 10) + new string('B', 50), Name = "chr1"
});
var baseSnippetSource = new GenomeSnippetSource("chr1", genome.Object, 20, 0);
var snippetSource = new ReusableSnippetSource(baseSnippetSource, 10);
var snippet = snippetSource.GetGenomeSnippet(5);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('A', 10) + new string('B', 30), snippet.Sequence);
Assert.Equal(0, snippet.StartPosition);
// Confirm proper indexing - demonstrates why we need to have 0 as min snippet startposition
var pair = TestHelpers.GetPair("10M", "10M");
pair.Read1.Bases = "AAAAAAAABB";
pair.Read1.Position = 5;
var originalAlignmentSummary =
Extensions.GetAlignmentSummary((new Read("chr1", pair.Read1)), snippet.Sequence, true, true, snippet.StartPosition);
Assert.Equal(3, originalAlignmentSummary.NumMismatches);
// Hitting up against the end of the chromosome
snippet = snippetSource.GetGenomeSnippet(59);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(21, snippet.Sequence.Length);
Assert.Equal(new string('B', 21), snippet.Sequence);
Assert.Equal(39, snippet.StartPosition);
// Very beginning of the chromosome
snippet = snippetSource.GetGenomeSnippet(0);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('A', 10) + new string('B', 30), snippet.Sequence);
Assert.Equal(0, snippet.StartPosition);
// Somewhere in the middle
snippet = snippetSource.GetGenomeSnippet(30);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('B', 40), snippet.Sequence);
Assert.Equal(10, snippet.StartPosition);
// Use the same snippet if we're close enough
snippet = snippetSource.GetGenomeSnippet(31);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('B', 40), snippet.Sequence);
Assert.Equal(10, snippet.StartPosition);
// Boundary: just within range to use the same snippet
snippet = snippetSource.GetGenomeSnippet(39);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('B', 40), snippet.Sequence);
Assert.Equal(10, snippet.StartPosition);
// Need to move to new snippet
snippet = snippetSource.GetGenomeSnippet(40);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('B', 40), snippet.Sequence);
Assert.Equal(20, snippet.StartPosition);
// Use the same snippet if we're close enough
snippet = snippetSource.GetGenomeSnippet(39);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('B', 40), snippet.Sequence);
Assert.Equal(20, snippet.StartPosition);
// Use the same snippet if we're close enough
snippet = snippetSource.GetGenomeSnippet(35);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('B', 40), snippet.Sequence);
Assert.Equal(20, snippet.StartPosition);
snippet = snippetSource.GetGenomeSnippet(31);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('B', 40), snippet.Sequence);
Assert.Equal(20, snippet.StartPosition);
snippet = snippetSource.GetGenomeSnippet(30);
Assert.Equal("chr1", snippet.Chromosome);
Assert.Equal(40, snippet.Sequence.Length);
Assert.Equal(new string('B', 40), snippet.Sequence);
Assert.Equal(10, snippet.StartPosition);
// Off the end of the chromosome
Assert.Throws <ArgumentException>(() => snippetSource.GetGenomeSnippet(81));
// Shouldn't have negative position
Assert.Throws <ArgumentException>(() => snippetSource.GetGenomeSnippet(-1));
}
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);
}
