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
}));