public void HappyPath()
{
//var bamFilePath = Path.Combine(TestPaths.SharedBamDirectory, "Chr17Chr19.bam");
//Assert.True(File.Exists(bamFilePath));
// TODO figure out how to access the shared bams
var tempPath = $"TemporaryBamFile_{Guid.NewGuid()}.bam";
if (File.Exists(tempPath))
{
File.Delete(tempPath);
}
using (var bamWriter = new BamWriter(tempPath, "header", new List <GenomeMetadata.SequenceMetadata>()))
{
bamWriter.WriteAlignment(TestHelpers.CreateBamAlignment("ATCG", 1, 10, 30, true));
}
var bamWriterFactory = new BamWriterFactory(1, tempPath);
var tempPath2 = $"TemporaryBamFile_{Guid.NewGuid()}.bam";
if (File.Exists(tempPath2))
{
File.Delete(tempPath2);
}
var bamWriterHandle = bamWriterFactory.CreateSingleBamWriter(tempPath2);
bamWriterHandle.WriteAlignment(TestHelpers.CreateBamAlignment("ATCAG", 1, 10, 30, true));
bamWriterHandle.WriteAlignment(null);
using (var reader = new BamReader(tempPath2))
{
// TODO more specific?
var header = reader.GetHeader();
Assert.Contains("ID:Gemini", header);
Assert.Contains("PN:Gemini", header);
}
File.Delete(tempPath);
File.Delete(tempPath2);
}
private IBamWriterFactory GetBamWriterFactory(string inBam)
{
var bamWriterFactory = new BamWriterFactory(_numThreads, inBam);
return(bamWriterFactory);
}
