public void TestJump()
{
var smallBam = Path.Combine(TestPaths.LocalTestDataDirectory, "bwaXC.bam");
using (var reader = new BamReader(smallBam))
{
BamAlignment al = new BamAlignment();
Assert.True(reader.Jump(reader.GetReferenceIndex("chr1"), 20200));
Assert.True(reader.GetNextAlignment(ref al, true));
Assert.True(al.Position > 18000);
Assert.True(reader.Jump(reader.GetReferenceIndex("chr1"), 200));
Assert.True(reader.GetNextAlignment(ref al, true));
Assert.True(al.Position < 250);
// now, forward-only jumping
Assert.True(reader.JumpForward(reader.GetReferenceIndex("chr1"), 20200));
Assert.True(reader.GetNextAlignment(ref al, true));
Assert.True(al.Position > 18000); // a good forward jump
var position = reader.Tell();
Assert.True(reader.JumpForward(reader.GetReferenceIndex("chr1"), 200));
Assert.Equal(position, reader.Tell()); // we stayed put
Assert.True(reader.GetNextAlignment(ref al, true));
Assert.True(al.Position > 18000);
}
}
