public void CreateBamReader()
{
// Should return a fully functional bam reader
var tempPath = $"TemporaryBamFile_{Guid.NewGuid()}.bam";
if (File.Exists(tempPath))
{
File.Delete(tempPath);
}
using (var bamWriter = new BamWriter(tempPath, "header", new List <GenomeMetadata.SequenceMetadata>()))
{
var bamWriterHandle = new BamWriterHandle(bamWriter);
bamWriterHandle.WriteAlignment(TestHelpers.CreateBamAlignment("ATCG", 8, 10, 30, true));
bamWriterHandle.WriteAlignment(null);
}
Assert.True(File.Exists(tempPath));
var stitcherOptions = new StitcherOptions();
var factory = new GeminiDataSourceFactory(stitcherOptions, "fakeGenomePath", false);
using (var bamReader = factory.CreateBamReader(tempPath))
{
BamAlignment alignment = new BamAlignment();
var getNext = bamReader.GetNextAlignment(ref alignment, true);
Assert.True(getNext);
Assert.Equal(7, alignment.Position);
}
File.Delete(tempPath);
}
public void HappyPath()
{
var tempPath = $"TemporaryBamFile_{Guid.NewGuid()}.bam";
if (File.Exists(tempPath))
{
File.Delete(tempPath);
}
using (var bamWriter = new BamWriter(tempPath, "header", new List <GenomeMetadata.SequenceMetadata>()))
{
var bamWriterHandle = new BamWriterHandle(bamWriter);
bamWriterHandle.WriteAlignment(TestHelpers.CreateBamAlignment("ATCG", 1, 10, 30, true));
bamWriterHandle.WriteAlignment(null);
}
Assert.True(File.Exists(tempPath));
File.Delete(tempPath);
}
