public void ExecuteTest(string inputBamFile, string outputBamFile, int expectedNumRealignedReads, int maxShift = 250)
{
if (File.Exists(outputBamFile))
{
File.Delete(outputBamFile);
}
var options = new HygeaOptions();
options.SkipAndRemoveDuplicates = false; //(old default/simple behavior for regression testing basic execution)
options.MaxRealignShift = maxShift;
var factory = new Factory(options);
var chrRef = GetGenomeSnippet();
var writer = new RemapBamWriter(inputBamFile, outputBamFile);
writer.Initialize();
var realigner = (ChrRealigner)factory.CreateRealigner(chrRef, inputBamFile, writer);
realigner.Execute();
writer.FinishAll();
Assert.True(File.Exists(outputBamFile));
Assert.Equal(expectedNumRealignedReads, realigner.TotalRealignedReads);
}
public void HappyPath()
{
if (!Directory.Exists(_outputDirectory))
{
Directory.CreateDirectory(_outputDirectory);
}
if (File.Exists(_outputFile))
{
File.Delete(_outputFile);
}
if (File.Exists(_outputFile + ".bai"))
{
File.Delete(_outputFile + ".bai");
}
var happyBamWriter = new RemapBamWriter(_bamFilePath, _outputFile, 10);
happyBamWriter.Initialize();
BamAlignment bam = CreateAlignment(10, 20, "Test");
happyBamWriter.WriteRead(ref bam, false);
happyBamWriter.FinishAll();
happyBamWriter.FlushAllBufferedRecords();
Assert.True(File.Exists(_outputFile));
Assert.True(File.Exists(_outputFile + ".bai"));
}
