コード例 #1
0
        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?
        }
コード例 #2
0
        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);
        }
コード例 #3
0
        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);
        }