public void ValidateErrorIndexingUnsortedBAM()
{
//samtools throws the following error, we should do the same
//[bam_index_core] the alignment is not sorted (H0KTMADXX130517:2:1111:17648:28366): 12370 > 12324 in 25-th chr
// Get filepath from xml config file.
string bamFilePath = this.utilityObj.xmlUtil.GetTextValue(
Constants.BAMUnsortedFilePath, Constants.FilePathNode);
using (Stream bamStream = new FileStream(bamFilePath, FileMode.Open, FileAccess.Read))
{
BAMParser parser = new BAMParser();
BAMIndex bamIndex;
try
{
bamIndex = parser.GetIndexFromBAMStorage(bamStream);
Assert.Fail();
}
catch(InvalidDataException)
{
}
catch(Exception) {
Assert.Fail();
}
finally
{
parser.Dispose();
}
}
// Log message to VSTest GUI.
ApplicationLog.WriteLine(string.Format(null,
"BAM Parser BVT : Validated error is thrown on indexing unsorted file"));
}
public void InvalidateGetIndexFromBAMFileUsingStream()
{
// Create BAM Parser object
using (var bamParserObj = new BAMParser())
{
try
{
bamParserObj.GetIndexFromBAMStorage(null);
Assert.Fail();
}
catch (ArgumentNullException ex)
{
string exceptionMessage = ex.Message;
ApplicationLog.WriteLine(string.Format(null,
"BAM Parser P2 : Validated Exception {0} successfully",
exceptionMessage));
}
}
}
/// <summary>
/// Creates BAMIndex object from the specified BAM file and writes to specified BAMIndex file.
/// </summary>
/// <param name="compressedBAMStream"></param>
/// <param name="indexStorage"></param>
private static void CreateBAMIndexFile(Stream compressedBAMStream, BAMIndexStorage indexStorage)
{
var parser = new BAMParser();
BAMIndex bamIndex = parser.GetIndexFromBAMStorage(compressedBAMStream);
indexStorage.Write(bamIndex);
}
public void ValidateBAMIndexMatchesExpectation()
{
// Get input and output values from xml node.
string BAMStoragePath = this.utilityObj.xmlUtil.GetTextValue(
Constants.BAMHumanLargeNode, Constants.FilePathNode);
string expectedIndexPath= this.utilityObj.xmlUtil.GetTextValue(
Constants.BAMHumanLargeNode, Constants.BAMIndexFileNode);
var bp = new BAMParser();
//get observed index file
BAMIndex bi;
using (Stream bamStream = new FileStream(BAMStoragePath, FileMode.Open, FileAccess.Read))
{
bi = bp.GetIndexFromBAMStorage(bamStream);
}
//get expected
var bi2 = new BAMIndexStorage(File.OpenRead(expectedIndexPath)).Read();
//now verify
Assert.AreEqual(bi2.RefIndexes.Count, bi.RefIndexes.Count);
for (int i = 0; i < bi.RefIndexes.Count; i++)
{
var obs = bi.RefIndexes[i];
var exp = bi2.RefIndexes[i];
Assert.AreEqual(obs.Bins.Count, exp.Bins.Count);
Assert.AreEqual(obs.LinearIndex.Count, exp.LinearIndex.Count);
Assert.AreEqual(obs.MappedReadsCount, exp.MappedReadsCount);
Assert.AreEqual(obs.UnMappedReadsCount, exp.UnMappedReadsCount);
var ob = obs.Bins.ToList();
var eb = exp.Bins.ToList();
ob.Sort((x, y) => x.BinNumber.CompareTo(y.BinNumber));
eb.Sort((x, y) => x.BinNumber.CompareTo(y.BinNumber));
for (int j = 0; j < ob.Count; j++)
{
var obb=ob[0];
var ebb=eb[0];
Assert.AreEqual(obb.BinNumber, ebb.BinNumber);
Assert.AreEqual(obb.Chunks.Count, ebb.Chunks.Count);
var c1 = obb.Chunks.ToList();
var c2 = ebb.Chunks.ToList();
c1.Sort((x, y) => x.ChunkStart.CompareTo(y.ChunkStart));
c2.Sort((x, y) => x.ChunkStart.CompareTo(y.ChunkStart));
for (int k = 0; k < c1.Count; k++)
{
var co = c1[k];
var eo = c2[k];
Assert.AreEqual(eo.ChunkStart, co.ChunkStart);
Assert.AreEqual(eo.ChunkEnd, co.ChunkEnd);
}
}
}
}