public static void Main(String[] args)
{
var aln = new BamAlignment();
var reader = new BamReader();
reader.Open(args[0]);
for (int i = 0; i < 10; i++)
{
reader.GetNextAlignment(aln);
Console.WriteLine("{0} {1}", aln.Name, aln.Length);
var foo = aln.CigarData[0];
}
}
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);
}
}
