private static void RunProcessorTest(string inBam, string outBam, string expBam, string outFolder, bool threadbyChr, StitcherOptions stitcherOptions)
{
if (File.Exists(outBam))
{
File.Delete(outBam);
}
Logger.OpenLog(TestPaths.LocalScratchDirectory, "StitcherTestLog.txt", true);
var processor = threadbyChr ? (IStitcherProcessor) new GenomeProcessor(inBam) : new BamProcessor();
processor.Process(inBam, outFolder, stitcherOptions);
Logger.CloseLog();
Assert.True(File.Exists(outBam));
var observedAlignment = new BamAlignment();
var expectedAlignment = new BamAlignment();
using (var outReader = new BamReader(outBam))
using (var expReader = new BamReader(expBam))
{
while (true)
{
var nextObservation = outReader.GetNextAlignment(ref observedAlignment, true);
var nextExpected = expReader.GetNextAlignment(ref expectedAlignment, true);
if ((nextExpected == false) || (expectedAlignment == null))
{
break;
}
Assert.Equal(expectedAlignment.Bases, observedAlignment.Bases);
Assert.Equal(expectedAlignment.Position, observedAlignment.Position);
Assert.Equal(expectedAlignment.Qualities, observedAlignment.Qualities);
}
outReader.Close();
expReader.Close();
}
}
public void TestMultithreaded()
{
BamAlignment bamAlignment = new BamAlignment()
{
Bases = "ACGT",
Bin = 0,
CigarData = new CigarAlignment("4M"),
Name = "Should have a constructor which initializes the members",
Position = 1,
Qualities = new byte[4],
TagData = new byte[4]
};
List <BamAlignment> bamAlignments = new List <BamAlignment>();
bamAlignments.Add(new BamAlignment(bamAlignment));
bamAlignment.Position = 2;
bamAlignments.Add(new BamAlignment(bamAlignment));
bamAlignment.Position = 10;
bamAlignments.Add(new BamAlignment(bamAlignment));
bamAlignment.Position = 11;
bamAlignments.Add(new BamAlignment(bamAlignment));
MemoryStream memoryBuffer = new MemoryStream();
var str = new Mock <MemoryStream>();
str.Setup(x => x.Write(It.IsAny <byte[]>(), It.IsAny <int>(), It.IsAny <int>())).Callback <byte[], int, int>((buffer, offset, count) =>
{ memoryBuffer.Write(buffer, offset, count); });
str.SetupGet(x => x.CanWrite).Returns(true);
using (var bamWriter = new BamWriterMultithreaded(
str.Object,
"",
new System.Collections.Generic.List <GenomeMetadata.SequenceMetadata>(),
2)) // 2 threads
{
var handles = bamWriter.GenerateHandles();
// Write 2 alignments on the first handle
// The positions are 1 and 10
handles[0].WriteAlignment(bamAlignments[0]);
handles[0].WriteAlignment(bamAlignments[2]);
// Write 2 alignments on the second handle
// The positions are 2 and 11
handles[1].WriteAlignment(bamAlignments[1]);
handles[1].WriteAlignment(bamAlignments[3]);
// This will sort and merge the alignments, and write the results to the stream
bamWriter.Flush();
}
memoryBuffer.Position = 0;
BamReader bamReader = new BamReader();
bamReader.Open(memoryBuffer);
var bamAlignmentsWritten = new List <BamAlignment>();
// Verify that all BamAlignment objects are found
// and they are in the right order.
for (int i = 0; i < 4; ++i)
{
BamAlignment al = new BamAlignment();
Assert.True(bamReader.GetNextAlignment(ref al, false));
bamAlignmentsWritten.Add(new BamAlignment(al));
}
bamReader.Close();
bamReader.Dispose();
bamAlignmentsWritten.Sort((al1, al2) => (al1.Position.CompareTo(al2.Position)));
for (int i = 0; i < 4; ++i)
{
Assert.Equal(bamAlignmentsWritten[i].Position, bamAlignments[i].Position);
}
}
