private void SetupMocksandExecute(IAlignmentExtractor extractorForRealign, IRealignmentWriter writer, bool skipDups, int maxShift, string chrReference = null, ITargetCaller targetCaller = null, IStateManager stateManager = null)
{
var extractorForCandidates = new Mock <IAlignmentExtractor>();
var ranker = new Mock <IIndelRanker>();
var indel = new CandidateIndel(new CandidateAllele("chr", 10, "C", "CTATATA", AlleleCategory.Insertion));
var indelFinder = new Mock <IIndelCandidateFinder>();
if (targetCaller == null)
{
var mocktargetCaller = new Mock <ITargetCaller>();
mocktargetCaller.Setup(x => x.Call(It.IsAny <List <CandidateIndel> >(), It.IsAny <IAlleleSource>()))
.Returns(new List <CandidateIndel>()
{
indel
});
targetCaller = mocktargetCaller.Object;
}
var realigner = new ChrRealigner(new ChrReference()
{
Sequence = chrReference ?? string.Join(string.Empty, Enumerable.Repeat("ACGT", 10))
}, extractorForCandidates.Object,
extractorForRealign, indelFinder.Object, ranker.Object, targetCaller,
new RealignStateManager(), writer, skipDuplicates: skipDups, maxRealignShift: maxShift);
realigner.Execute();
}
private void SetupExecute(IAlignmentExtractor extractorForRealign, IAlignmentExtractor extractorForCandidates, MockRealignmentWriter writer,
bool skipDups, int maxShift, string chrReference = null, float frequencyCutoff = 0, bool skipAndRemove = false, Action <IEnumerable <BamAlignment> > verifyRemappedReads = null, bool allowRescoringOrig0 = true, int realignWindowSize = 1000)
{
var ranker = new Mock <IIndelRanker>();
var realigner = new ChrRealigner(new ChrReference()
{
Name = "chr", Sequence = chrReference ?? string.Join(string.Empty, Enumerable.Repeat("ACGT", 10))
},
extractorForCandidates,
extractorForRealign, new IndelTargetFinder(0), ranker.Object,
new IndelTargetCaller(frequencyCutoff),
new RealignStateManager(realignWindowSize: realignWindowSize), writer, skipDuplicates: skipDups, skipAndRemoveDuplicates: skipAndRemove, maxRealignShift: maxShift, allowRescoringOrig0: allowRescoringOrig0);
realigner.Execute();
Assert.Equal(writer.ReadsExpected, writer.ReadsWritten);
verifyRemappedReads?.Invoke(writer.RemappedReads);
}