public void RefMinorSearch()
{
var saIndex = new SaIndex(3);
var nodeCount = 3 * SaIndexNode.SaNodeWidth;
for (uint i = 0; i < nodeCount; i++)
{
saIndex.Add(100 + i * 3, 1000 + i * 30, i % 3 == 0);//every third item is ref minor
}
var randomPath = GetRandomPath();
saIndex.Write(randomPath, "chr1");
using (var reader = new ExtendedBinaryReader(FileUtilities.GetReadStream(randomPath)))
{
var readSaIndex = new SaIndex(reader);
Assert.True(readSaIndex.IsRefMinor(100));
//this result should be cached for the next query
Assert.Equal((uint)1000, readSaIndex.GetFileLocation(100));
Assert.False(readSaIndex.IsRefMinor(101));//not present position
Assert.Equal((uint)1030, readSaIndex.GetFileLocation(103));
//this result should be cached for the next query
Assert.True(readSaIndex.IsRefMinor(109));
Assert.Equal(uint.MinValue, readSaIndex.GetFileLocation(131));//location past the index
}
File.Delete(randomPath);
}
public void IndexCreation()
{
var saIndex = new SaIndex(3);
var nodeCount = 3 * SaIndexNode.SaNodeWidth;
for (uint i = 0; i < nodeCount; i++)
{
saIndex.Add(100 + i, 1000 + i * 19, false);
}
Assert.Equal(Math.Ceiling(nodeCount * 1.0 / (SaIndexNode.SaNodeWidth + 1)), saIndex.Count());
}
public RefMinorProvider(List <string> supplementaryAnnotationDirectories)
{
foreach (var directory in supplementaryAnnotationDirectories)
{
foreach (var file in Directory.GetFiles(directory, "*.idx"))
{
var chromeName = Path.GetFileNameWithoutExtension(file).Split('.')[0];
var refMinorPostions = SaIndex.Read(FileUtilities.GetReadStream(file)).GlobalMajorAlleleForRefMinor;
if (refMinorPostions.Length > 0)
{
_positionDict[chromeName] = refMinorPostions.ToDictionary(x => x.Position, x => x.GlobalMajorAllele);
}
}
}
}
public void IndexWriteRead()
{
var saIndex = new SaIndex(3);
var nodeCount = 3 * SaIndexNode.SaNodeWidth;
for (uint i = 0; i < nodeCount; i++)
{
saIndex.Add(100 + i, 1000 + i * 19, i % 3 == 0);//every third node is ref minor
}
var randomPath = GetRandomPath();
saIndex.Write(randomPath, "chr1");
using (var reader = new ExtendedBinaryReader(FileUtilities.GetReadStream(randomPath)))
{
var readSaIndex = new SaIndex(reader);
Assert.Equal(Math.Ceiling(nodeCount * 1.0 / (SaIndexNode.SaNodeWidth + 1)), readSaIndex.Count());
Assert.Equal("chr1", readSaIndex.RefSeqName);
}
File.Delete(randomPath);
}
