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 FindLargeVaritants_method_does_not_return_small_variants()
{
var index = new JasixIndex();
index.Add("chr1", 100, 101, 100_000);
index.Add("chr1", 105, 109, 100_050);
index.Add("chr1", 160, 166, 100_100);
index.Add("chr1", 200, 1000, 100_075);//large variant
index.Add("chr2", 100, 100, 100_150);
index.Add("chr2", 102, 105, 100_200);
index.Flush();
//checking large variants
Assert.Null(index.LargeVariantPositions("chr1", 100, 199));
var largeVariants = index.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 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
}));