private void ExecuteTest_ProcessReadsSeparately(bool doMate, bool doStitch)
{
var read = CreateRead("chr1", "ACGT", 10, "read1", matePosition: 100);
var readMate = CreateRead("chr1", "ACGT", 100, "read1", read2: true, matePosition: 10);
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, config);
var alignmentSet = source.GetNextRead();
// TODO what do we really want to test here now that we're not pairing?
}
public void GetAlignmentSet()
{
var reads = new List <Read>();
reads.Add(CreateRead("chr1", "ACGT", 10, "read1", matePosition: 10));
reads.Add(CreateRead("chr1", "ACGT", 10, "read2", matePosition: 10));
reads.Add(CreateRead("chr1", "ACGT", 10, "read1", read2: true, matePosition: 10)); // mate
reads.Add(CreateRead("chr1", "ACGT", 10, "read_notmapped", isMapped: false, isProperPair: false, matePosition: 10));
reads.Add(CreateRead("chr1", "ACGT", 10, "read3", isProperPair: false, read2: true, matePosition: 10)); // mate
reads.Add(CreateRead("chr1", "ACGT", 10, "read2", read2: true, matePosition: 10));
var extractor = new MockAlignmentExtractor(reads);
var config = new AlignmentSourceConfig {
MinimumMapQuality = 10, OnlyUseProperPairs = false
};
var source = new AlignmentSource(extractor, null, config);
Read read;
var numSets = 0;
while ((read = source.GetNextRead()) != null)
{
numSets++;
Assert.False(read.Name == "read_notmapped");
}
Assert.Equal(numSets, 5);
}
public void Filtering()
{
//bool isMapped = true, bool isPrimaryAlignment = true, bool isProperPair = true, bool isDuplicate = false
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, SkipDuplicates = true
};
var source = new AlignmentSource(extractor, null, config);
Read read;
var fetchedCount = 0;
while ((read = source.GetNextRead()) != null)
{
fetchedCount++;
Assert.Equal(read.Name, "yay");
}
Assert.Equal(1, fetchedCount);
// -------------------------
// turn off proper pairs
config.OnlyUseProperPairs = false;
fetchedCount = 0;
extractor.Reset();
source = new AlignmentSource(extractor, null, config);
while ((read = source.GetNextRead()) != null)
{
fetchedCount++;
Assert.Equal(read.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, config);
while ((read = source.GetNextRead()) != null)
{
fetchedCount++;
Assert.Equal(read.Name,
fetchedCount == 1 ? "filtered_quality" : "yay");
}
Assert.Equal(fetchedCount, 2);
}