private TransformManyBlock <IEnumerable <ReadPair>, PairResult> GetPairClassifierBlock()
{
var readPair = new TransformManyBlock <IEnumerable <ReadPair>, PairResult>(
(data) =>
{
var classifier = new ReadPairClassifierAndExtractor(_geminiOptions.TrustSoftclips,
(int)_stitcherOptions.FilterMinMapQuality, skipStitch: _geminiOptions.SkipStitching, treatAbnormalOrientationAsImproper: _geminiOptions.TreatAbnormalOrientationAsImproper, messyMapq: _geminiOptions.MessyMapq, numSoftclipsToBeConsideredMessy: _geminiOptions.NumSoftclipsToBeConsideredMessy, numMismatchesToBeConsideredMessy: _geminiOptions.NumMismatchesToBeConsideredMessy, stringTagsToKeepFromR1: _stitcherOptions.StringTagsToKeepFromR1, checkMd: _geminiOptions.SilenceSuspiciousMdReads);
var pairHandler = GetPairHandler(_refIdMapping);
// Get batches from groups
var batches = new List <PairResult>();
foreach (var pair in data)
{
var pairResult = classifier.GetBamAlignmentsAndClassification(pair, pairHandler);
if (pairResult.Classification != PairClassification.Unusable &&
pairResult.Classification != PairClassification.UnusableSplit &&
(!_geminiOptions.SkipAndRemoveDups || pairResult.Classification != PairClassification.Duplicate))
{
batches.Add(pairResult);
}
}
//pairHandler.Finish();
return(batches);
}, new ExecutionDataflowBlockOptions()
{
MaxDegreeOfParallelism = _maxDegreeOfParallelism,
EnsureOrdered = true
}
);
return(readPair);
}
private void VerifyClassificationAndExtraction(ReadPair readpair, PairClassification expectedClassification,
int expectedNumReads, bool trustSoftclips, bool deferStitchIndelReads = true, bool shouldTryStitch = true, bool stageStitchSucceed = true, bool treatAbnormalOrientationAsImproper = false,
int messyMapq = 30, bool checkMd = false)
{
var pairHandler = new Mock <IReadPairHandler>();
pairHandler.Setup(x => x.ExtractReads(It.IsAny <ReadPair>())).Returns(stageStitchSucceed
? new List <BamAlignment>()
{
readpair.Read1
}
: new List <BamAlignment>()
{
readpair.Read1, readpair.Read2
});
var extractor = new ReadPairClassifierAndExtractor(trustSoftclips,
messyMapq: messyMapq, treatAbnormalOrientationAsImproper: treatAbnormalOrientationAsImproper, checkMd: checkMd);
var result = extractor.GetBamAlignmentsAndClassification(readpair, pairHandler.Object);
var alignments = result.Alignments;
Assert.Equal(expectedClassification, result.Classification);
pairHandler.Verify(x => x.ExtractReads(It.IsAny <ReadPair>()), Times.Exactly(shouldTryStitch ? 1 : 0));
Assert.Equal(expectedNumReads, alignments.ToList().Count);
}
