public void BamWriterHandle()
{
var writerFactory = new Mock <IBamWriterFactory>();
var writers = new List <Mock <IBamWriterHandle> >();
writerFactory.Setup(x => x.CreateSingleBamWriter(It.IsAny <string>())).Returns <string>(s =>
{
var bamWriter = new Mock <IBamWriterHandle>();
writers.Add(bamWriter);
return(bamWriter.Object);
});
var writerSource = new WriterSourceRecycled("outbam", writerFactory.Object);
var handle1 = writerSource.BamWriterHandle("chr1", PairClassification.Disagree, 1);
writerFactory.Verify(x => x.CreateSingleBamWriter(It.IsAny <string>()), Times.Exactly(1));
var handle2 = writerSource.BamWriterHandle("chr1", PairClassification.Disagree, 1);
writerFactory.Verify(x => x.CreateSingleBamWriter(It.IsAny <string>()), Times.Exactly(2));
Assert.NotEqual(handle1, handle2);
writerSource.DoneWithWriter("chr1", PairClassification.Disagree, 1, 10, handle1);
// Handle1 should be recycled
var handle3 = writerSource.BamWriterHandle("chr1", PairClassification.Disagree, 1);
writerFactory.Verify(x => x.CreateSingleBamWriter(It.IsAny <string>()), Times.Exactly(2));
Assert.Equal(handle1, handle3);
}
public void Finish()
{
var writerFactory = new Mock <IBamWriterFactory>();
var writers = new List <Mock <IBamWriterHandle> >();
writerFactory.Setup(x => x.CreateSingleBamWriter(It.IsAny <string>())).Returns <string>(s =>
{
var bamWriter = new Mock <IBamWriterHandle>();
writers.Add(bamWriter);
return(bamWriter.Object);
});
var writerSource = new WriterSourceRecycled("outbam", writerFactory.Object);
var handle1 = writerSource.BamWriterHandle("chr1", PairClassification.Disagree, 1);
writerFactory.Verify(x => x.CreateSingleBamWriter(It.IsAny <string>()), Times.Exactly(1));
var handle2 = writerSource.BamWriterHandle("chr1", PairClassification.Disagree, 1);
writerFactory.Verify(x => x.CreateSingleBamWriter(It.IsAny <string>()), Times.Exactly(2));
Assert.Equal(2, writers.Count);
foreach (var writer in writers)
{
writer.Verify(x => x.WriteAlignment(null), Times.Never);
}
writerSource.Finish();
foreach (var writer in writers)
{
writer.Verify(x => x.WriteAlignment(null), Times.Once);
}
Assert.Equal(2, writerSource.GetBamFiles().Count);
}
public IWriterSource GetWriterSource(string inBam, string outBam)
{
var writerFactory = GetBamWriterFactory(inBam);
var writerSource =
new WriterSourceRecycled(outBam, writerFactory);
return(writerSource);
}
