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);
}
}
private bool JumpIfNeeded(List <Region> chrIntervals, out Region currentRegion)
{
var completedIntervals = new List <Region>();
for (var i = 0; i < chrIntervals.Count; i++)
{
var interval = chrIntervals[i];
if ((_rawAlignment.Position + 1) > interval.EndPosition) // bam alignment is 0-based, interval is 1-based
{
completedIntervals.Add(interval);
_shouldCheckJumpForCurrentInterval = true;
}
else
{
break;
}
}
foreach (var completedInterval in completedIntervals)
{
chrIntervals.Remove(completedInterval);
}
// if done with intervals, jump to next chromosome
if (!chrIntervals.Any())
{
currentRegion = null;
if (_rawAlignment.RefID == _references.Count - 1)
{
return(false);
}
if (_mateFinder == null || _mateFinder.NextMatePosition == null)
{
return(_bamReader.Jump(_rawAlignment.RefID + 1, 0));
}
return(true);
}
currentRegion = chrIntervals[0];
// if far from next interval, jump forward. leave small buffer so we dont accidentally re-read already read alignments if there's not much gap inbetween
if (_shouldCheckJumpForCurrentInterval)
{
var targetInterval = currentRegion;
const int buffer = 100;
var refMaxIndex = (int)(_references.First(r => r.Index == _rawAlignment.RefID).Length - 1);
var jumpToThreshold = Math.Min(Math.Max(0, targetInterval.StartPosition - buffer), refMaxIndex);
if (_mateFinder != null)
{
var nextMate = _mateFinder.NextMatePosition;
if (nextMate != null && nextMate.Value < jumpToThreshold)
{
jumpToThreshold = nextMate.Value;
}
else
{
_shouldCheckJumpForCurrentInterval = false;
}
}
else
{
_shouldCheckJumpForCurrentInterval = false;
}
if ((_rawAlignment.GetEndPosition() - _rawAlignment.CigarData.GetSuffixClip()) < jumpToThreshold)
{
return(_bamReader.JumpForward(_rawAlignment.RefID, Math.Min(Math.Max(0, targetInterval.StartPosition - 1), refMaxIndex)));
}
}
return(true);
}
