private static List <ReadPair> GetReadPairs(List <BamAlignment> bamAlignments, Dictionary <BamAlignment, ReadPair> stagedReadPairs, List <BamAlignment> flushableUnpaired, bool skipDups, int?refId = null, int?readLength = null)
{
var refIdLookup = new Dictionary <string, int>()
{
{ "chr1", 1 }
};
var bamReader = new MockBamReader(bamAlignments, refIdLookup);
var mockFilter = new Mock <IAlignmentPairFilter>();
mockFilter.Setup(x => x.TryPair(It.IsAny <BamAlignment>(), It.IsAny <PairStatus>())).Returns <BamAlignment, PairStatus>((b, p) => stagedReadPairs[b]);
mockFilter.Setup(x => x.GetFlushableUnpairedReads()).Returns(flushableUnpaired);
var source = new PairFilterReadPairSource(bamReader, new ReadStatusCounter(), skipDups,
mockFilter.Object, refId: refId, expectedFragmentLength: readLength);
var readPairs = new List <ReadPair>();
while (true)
{
var readPair = source.GetNextEntryUntilNull();
if (readPair == null)
{
break;
}
readPairs.Add(readPair);
}
return(readPairs);
}
public void GetNextEntryUntilNull_NonMocked()
{
var readEarly = TestHelpers.CreateBamAlignment(new string('A', 100), 3, 500, 30, false, name: "FarApart", isFirstMate: true);
readEarly.FragmentLength = 600;
readEarly.SetIsPaired(true);
var readLate = TestHelpers.CreateBamAlignment(new string('A', 100), 500, 3, 30, false, name: "FarApart", isFirstMate: true);
readLate.FragmentLength = -600;
readLate.SetIsPaired(true);
var bamAlignments = new List <BamAlignment>()
{
readEarly, readLate
};
var refIdLookup = new Dictionary <string, int>()
{
{ "chr1", 1 }
};
var bamReader = new MockBamReader(bamAlignments, refIdLookup);
var filter = new StitcherPairFilter(false,
false, new AlignmentFlagDuplicateIdentifier(), new ReadStatusCounter(),
minMapQuality: 0, treatImproperAsIncomplete: false);
var source = new PairFilterReadPairSource(bamReader, new ReadStatusCounter(), false,
filter, refId: 1, expectedFragmentLength: 150);
// Return far apart reads individually so we don't bog down memory with things that don't act as pairs (stitch, cover same indels) anyway.
var nextEntry = source.GetNextEntryUntilNull();
Assert.Equal(2, nextEntry.MinPosition);
Assert.Equal(1, nextEntry.NumPrimaryReads);
Assert.Equal(PairStatus.LongFragment, nextEntry.PairStatus);
nextEntry = source.GetNextEntryUntilNull();
Assert.Equal(499, nextEntry.MinPosition);
Assert.Equal(1, nextEntry.NumPrimaryReads);
Assert.Equal(PairStatus.LongFragment, nextEntry.PairStatus);
}
