public void GetAlignmentSet()
{
var reads = new List <Read>();
reads.Add(CreateRead("chr1", "ACGT", 1, "read1"));
reads.Add(CreateRead("chr1", "ACGT", 1, "read2"));
reads.Add(CreateRead("chr1", "ACGT", 1, "read1_mate"));
reads.Add(CreateRead("chr1", "ACGT", 1, "read3_unmapped", isMapped: false, isProperPair: false));
reads.Add(CreateRead("chr1", "ACGT", 1, "read3_mate", isProperPair: false));
reads.Add(CreateRead("chr1", "ACGT", 1, "read2_mate"));
var extractor = new MockAlignmentExtractor(reads);
var mateFinder = new Mock <IAlignmentMateFinder>();
mateFinder.Setup(f => f.GetMate(It.IsAny <Read>())).Returns(
(Read r) =>
r.Name.EndsWith("_mate")
? reads.FirstOrDefault(o => o.Name == r.Name.Replace("_mate", string.Empty))
: null);
var stitcher = new Mock <IAlignmentStitcher>();
stitcher.Setup(s => s.TryStitch(It.IsAny <AlignmentSet>())).Callback((AlignmentSet s) => s.IsStitched = true);
var config = new AlignmentSourceConfig {
MinimumMapQuality = 10, OnlyUseProperPairs = false
};
var source = new AlignmentSource(extractor, mateFinder.Object, stitcher.Object, config);
AlignmentSet set;
var numSets = 0;
while ((set = source.GetNextAlignmentSet()) != null)
{
numSets++;
if (!set.IsFullPair)
{
Assert.True(set.PartnerRead1.Name.Equals("read3_mate"));
Assert.True(set.PartnerRead2 == null);
Assert.False(set.IsStitched);
}
else
{
Assert.True(set.PartnerRead2.Name.Equals(set.PartnerRead1.Name + "_mate"));
Assert.True(set.IsStitched);
}
}
Assert.Equal(numSets, 3);
}
private void ExecuteTest_ProcessReadsSeparately(bool doMate, bool doStitch)
{
var read = CreateRead("chr1", "ACGT", 1, "read1");
var readMate = CreateRead("chr1", "ACGT", 10, "read1mate");
var extractor = new MockAlignmentExtractor(new List <Read>()
{
read
});
var mateFinder = new Mock <IAlignmentMateFinder>();
mateFinder.Setup(f => f.GetMate(It.IsAny <Read>())).Returns(readMate);
var stitcher = new Mock <IAlignmentStitcher>();
var config = new AlignmentSourceConfig {
MinimumMapQuality = 10, OnlyUseProperPairs = false
};
var source = new AlignmentSource(extractor, doMate ? mateFinder.Object : null, doStitch ? stitcher.Object : null, config);
var alignmentSet = source.GetNextAlignmentSet();
// verify stitching relies on pairing
stitcher.Verify(s => s.TryStitch(It.IsAny <AlignmentSet>()), Times.Never);
if (!doMate)
{
TestHelper.CompareReads(read, alignmentSet.PartnerRead1);
Assert.Equal(null, alignmentSet.PartnerRead2);
Assert.Equal(1, alignmentSet.ReadsForProcessing.Count);
TestHelper.CompareReads(read, alignmentSet.ReadsForProcessing.First());
}
else
{
TestHelper.CompareReads(read, alignmentSet.PartnerRead1);
TestHelper.CompareReads(readMate, alignmentSet.PartnerRead2);
Assert.Equal(2, alignmentSet.ReadsForProcessing.Count);
TestHelper.CompareReads(read, alignmentSet.ReadsForProcessing.First());
TestHelper.CompareReads(readMate, alignmentSet.ReadsForProcessing.Last());
}
}
public void Filtering()
{
var reads = new List <Read>();
reads.Add(CreateRead("chr1", "AAA", 1, "filtered", false, true, true, false, 10));
reads.Add(CreateRead("chr1", "AAA", 1, "filtered", true, false, true, false, 10));
reads.Add(CreateRead("chr1", "AAA", 1, "filtered_properpair", true, true, false, false, 10));
reads.Add(CreateRead("chr1", "AAA", 1, "filtered", true, true, true, true, 10));
reads.Add(CreateRead("chr1", "AAA", 1, "filtered_quality", true, true, true, false, 9));
reads.Add(CreateRead("chr1", "AAA", 1, "Filtered_CigarData", true, true, true, false, 10, false));
reads.Add(CreateRead("chr1", "AAA", 1, "yay", true, true, true, false, 10));
var extractor = new MockAlignmentExtractor(reads);
var config = new AlignmentSourceConfig {
MinimumMapQuality = 10, OnlyUseProperPairs = true
};
var source = new AlignmentSource(extractor, null, null, config);
AlignmentSet set;
var fetchedCount = 0;
while ((set = source.GetNextAlignmentSet()) != null)
{
fetchedCount++;
Assert.Equal(set.PartnerRead1.Name, "yay");
}
Assert.Equal(1, fetchedCount);
// -------------------------
// turn off proper pairs
config.OnlyUseProperPairs = false;
fetchedCount = 0;
extractor.Reset();
source = new AlignmentSource(extractor, null, null, config);
while ((set = source.GetNextAlignmentSet()) != null)
{
fetchedCount++;
Assert.Equal(set.PartnerRead1.Name,
fetchedCount == 1 ? "filtered_properpair" : "yay");
}
Assert.Equal(fetchedCount, 2);
// -------------------------
// change quality cut off
config.OnlyUseProperPairs = true;
config.MinimumMapQuality = 9;
fetchedCount = 0;
extractor.Reset();
source = new AlignmentSource(extractor, null, null, config);
while ((set = source.GetNextAlignmentSet()) != null)
{
fetchedCount++;
Assert.Equal(set.PartnerRead1.Name,
fetchedCount == 1 ? "filtered_quality" : "yay");
}
Assert.Equal(fetchedCount, 2);
}