public void IndexCreation_multiChromosome() { var jsonStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("cosmicv72.indels.json.gz")), CompressionMode.Decompress); var writeStream = new MemoryStream(); using (var indexCreator = new IndexCreator(jsonStream, writeStream)) { indexCreator.CreateIndex(); } JasixIndex readBackIndex; var readStream = new MemoryStream(writeStream.ToArray()); readStream.Seek(0, SeekOrigin.Begin); using (readStream) { readBackIndex = new JasixIndex(readStream); } Assert.Equal(2268, readBackIndex.GetFirstVariantPosition("chr1", 9775924, 9775924)); Assert.Equal(14035925971, readBackIndex.GetFirstVariantPosition("chr2", 16081096, 16081096)); Assert.Equal(433156622693, readBackIndex.GetFirstVariantPosition("chr20", 36026164, 36026164)); Assert.Equal(439602269527, readBackIndex.GetFirstVariantPosition("chrX", 66765044, 66765044)); }
public void Add_one_chrom() { var position1 = new Mock <IPosition>(); position1.SetupGet(x => x.Chromosome).Returns(ChromosomeUtilities.Chr1); position1.SetupGet(x => x.Start).Returns(100); position1.SetupGet(x => x.RefAllele).Returns("A"); position1.SetupGet(x => x.AltAlleles).Returns(new [] { "C" }); var memStream = new MemoryStream(); using (var indexCreator = new OnTheFlyIndexCreator(memStream)) { indexCreator.BeginSection("positions", 100); indexCreator.Add(position1.Object, 2588); indexCreator.EndSection("positions", 2699); } var readStream = new MemoryStream(memStream.ToArray()); readStream.Seek(0, SeekOrigin.Begin); var index = new JasixIndex(readStream); Assert.Equal(100, index.GetSectionBegin("positions")); Assert.Equal(2588, index.GetFirstVariantPosition("chr1", 100, 102)); }
public void GetFirstVariantPosition_multi_chrom_index() { var index = new JasixIndex(); index.Add("chr1", 100, 101, 100000); index.Add("chr1", 105, 109, 100050); index.Add("chr1", 160, 166, 100100); index.Add("chr2", 100, 100, 100150); index.Add("chr2", 102, 105, 100200); index.Flush(); var chrPos = Utilities.ParseQuery("chr1"); Assert.Equal(100000, index.GetFirstVariantPosition(chrPos.Item1, chrPos.Item2, chrPos.Item3)); chrPos = Utilities.ParseQuery("chr2"); Assert.Equal(100150, index.GetFirstVariantPosition(chrPos.Item1, chrPos.Item2, chrPos.Item3)); }
public void Write_and_read_back() { var index = new JasixIndex(); index.Add("chr1", 100, 101, 100000, "1"); index.Add("chr1", 105, 109, 100050, "1"); index.Add("chr1", 150, 1000, 100075, "1");//large variant index.Add("chr1", 160, 166, 100100, "1"); index.Add("chr2", 100, 100, 100150, "2"); index.Add("chr2", 102, 105, 100200, "2"); var writeStream = new MemoryStream(); using (writeStream) { index.Write(writeStream); } var readStream = new MemoryStream(writeStream.ToArray()); readStream.Seek(0, SeekOrigin.Begin); JasixIndex readBackIndex; using (readStream) { readBackIndex = new JasixIndex(readStream); } Assert.Equal(100000, readBackIndex.GetFirstVariantPosition("chr1", 100, 102)); Assert.Equal(100000, readBackIndex.GetFirstVariantPosition("chr1", 103, 104)); Assert.Equal(100000, readBackIndex.GetFirstVariantPosition("chr1", 120, 124)); Assert.Equal(100000, readBackIndex.GetFirstVariantPosition("chr1", 158, 160)); Assert.Equal(100150, readBackIndex.GetFirstVariantPosition("chr2", 103, 105)); //checking large variants Assert.Null(readBackIndex.LargeVariantPositions("chr1", 100, 149)); var largeVariants = readBackIndex.LargeVariantPositions("chr1", 100, 201); Assert.NotNull(largeVariants); Assert.Single(largeVariants); Assert.Equal(100075, largeVariants[0]); }
public void IndexWriteRead() { var index = new JasixIndex(); index.Add("chr1", 100, 101, 100000); index.Add("chr1", 105, 109, 100050); index.Add("chr1", 150, 1000, 100075);//large variant index.Add("chr1", 160, 166, 100100); index.Add("chr2", 100, 100, 100150); index.Add("chr2", 102, 105, 100200); var tempFile = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName()); using (var writer = FileUtilities.GetCreateStream(tempFile)) { index.Write(writer); } JasixIndex readBackIndex; using (var stream = FileUtilities.GetReadStream(tempFile)) { readBackIndex = new JasixIndex(stream); } File.Delete(tempFile); Assert.Equal(100000, readBackIndex.GetFirstVariantPosition("chr1", 100, 102)); Assert.Equal(100000, readBackIndex.GetFirstVariantPosition("chr1", 103, 104)); Assert.Equal(100000, readBackIndex.GetFirstVariantPosition("chr1", 120, 124)); Assert.Equal(100000, readBackIndex.GetFirstVariantPosition("chr1", 158, 160)); Assert.Equal(100150, readBackIndex.GetFirstVariantPosition("chr2", 103, 105)); //checking large variants Assert.Null(readBackIndex.LargeVariantPositions("chr1", 100, 149)); var largeVariants = readBackIndex.LargeVariantPositions("chr1", 100, 201); Assert.NotNull(largeVariants); Assert.Single(largeVariants); Assert.Equal(100075, largeVariants[0]); }
public void Add_fill_node_and_start_another() { var index = new JasixIndex(); //creating two nodes each containing 50 entries for (var i = 0; i < 2 * JasixCommons.PreferredNodeCount; i++) { index.Add("chr1", 100 + i, 101 + i, 100_000 + i); } index.Add("chr1", 160 + 2 * JasixCommons.PreferredNodeCount, 166 + 2 * JasixCommons.PreferredNodeCount, 200_100); index.Add("chr2", 100, 100, 200_150); index.Add("chr2", 102, 105, 200_200); index.Flush(); Assert.Equal(100_000, index.GetFirstVariantPosition("chr1", 100, 102)); Assert.Equal(100_000 + JasixCommons.PreferredNodeCount, index.GetFirstVariantPosition("chr1", 2 * JasixCommons.PreferredNodeCount + 55, 2 * JasixCommons.PreferredNodeCount + 55)); Assert.Equal(-1, index.GetFirstVariantPosition("chr1", 2 * JasixCommons.PreferredNodeCount + 120, 2 * JasixCommons.PreferredNodeCount + 124)); Assert.Equal(200_100, index.GetFirstVariantPosition("chr1", 2 * JasixCommons.PreferredNodeCount + 158, 2 * JasixCommons.PreferredNodeCount + 160)); Assert.Equal(200_150, index.GetFirstVariantPosition("chr2", 103, 105)); }
public void TestIndexCreation() { var readStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("cosmicv72.indels.json.gz")), CompressionMode.Decompress); var tempFile = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName()); using (var indexCreator = new IndexCreator(readStream, FileUtilities.GetCreateStream(tempFile))) { indexCreator.CreateIndex(); } JasixIndex readBackIndex; using (var stream = FileUtilities.GetReadStream(tempFile)) { readBackIndex = new JasixIndex(stream); } Assert.Equal(1591, readBackIndex.GetFirstVariantPosition("chr1", 9775924, 9775924)); Assert.Equal(11500956299, readBackIndex.GetFirstVariantPosition("chr2", 16081096, 16081096)); Assert.Equal(372100991296, readBackIndex.GetFirstVariantPosition("chr20", 36026164, 36026164)); Assert.Equal(377682846863, readBackIndex.GetFirstVariantPosition("chrX", 66765044, 66765044)); File.Delete(tempFile); }
public void Combination_of_large_and_small_variants() { var index = new JasixIndex(); //query range 10,000- 10,020 index.Add("chr1", 8_000, 9_900, 90_000); //SV not overlapping the query index.Add("chr1", 9_000, 10_005, 90_100); // partially overlapping index.Add("chr1", 9_500, 10_050, 90_200); //completely overlapping index.Add("chr1", 10_000, 10_001, 100_000); index.Add("chr1", 10_004, 10_006, 100_100); index.Add("chr1", 10_009, 10_550, 100_200);//SV starting from the middle of the range index.Add("chr1", 10_008, 10_010, 100_300); index.Add("chr1", 10_011, 10_020, 100_400); index.Add("chr1", 10_039, 10_550, 100_200);//SV past the range index.Flush(); var firstSmallVarLocation = index.GetFirstVariantPosition("chr1", 10_000, 10_020); var largeVariantLocations = index.LargeVariantPositions("chr1", 10_000, 10_020); Assert.Equal(90_000, firstSmallVarLocation); Assert.True(largeVariantLocations.SequenceEqual(new List <long> { 90_100, 90_200, 100_200 }));