/// <summary>
/// returns true if the alignment overlaps with the specified interval
/// </summary>
private bool IsOverlap(int begin, int end, BamAlignment alignment)
{
int alignmentBegin = alignment.Position;
int alignmentEnd = alignment.GetEndPosition();
return((alignmentEnd >= begin) && (alignmentBegin < end));
}
/// <summary>
/// Adds an offset to a specific reference sequence in the index
/// </summary>
private static void AddOffset(ref List <ulong> offsets, ref BamAlignment al, ulong offset)
{
int beg = al.Position >> BamLidxShift;
int end = (al.GetEndPosition() - 1) >> BamLidxShift;
// initialize additional entries if needed
while (offsets.Count < (end + 1))
{
offsets.Add(0);
}
if (beg == end)
{
if (offsets[beg] == 0)
{
offsets[beg] = offset;
}
}
else
{
for (int i = beg; i <= end; i++)
{
if (offsets[i] == 0)
{
offsets[i] = offset;
}
}
}
}
/// <summary>
/// returns true if the alignment overlaps with the specified interval [<paramref name="begin"/>,<paramref name="end"/>)
/// </summary>
/// <param name="begin">Start of the interval. By default inclusive.</param>
/// <param name="end">End of the interval. By default exclusive.</param>
/// <param name="alignment"></param>
/// <param name="inclusiveEnd">If true, test overlap in the interval [<paramref name="begin"/>,<paramref name="end"/>] </param>
private bool IsOverlap(int begin, int end, BamAlignment alignment, bool inclusiveEnd = false)
{
int alignmentBegin = alignment.Position;
int alignmentEnd = alignment.GetEndPosition();
return((alignmentEnd >= begin) && ((inclusiveEnd && alignmentBegin <= end) || (!inclusiveEnd && alignmentBegin < end)));
}
public void GetEndPosition_Tests()
{
var alignment1 = new BamAlignment()
{
Position = 500,
CigarData = new CigarAlignment("5M7I19M3D")
};
Assert.Equal(526, alignment1.GetEndPosition());
var alignmentWithNoMappingBases = new BamAlignment()
{
Position = 500,
CigarData = new CigarAlignment("3I")
};
//Assert.Equal(500, alignment2.GetEndPosition());
// Apparently for a degenerate case such as this, we're going to allow start position to be > end position.
// https://jira.illumina.com/browse/PICS-857
Assert.Equal(499, alignmentWithNoMappingBases.GetEndPosition());
alignmentWithNoMappingBases = new BamAlignment()
{
Position = 500,
CigarData = new CigarAlignment("100S")
};
Assert.Equal(499, alignmentWithNoMappingBases.GetEndPosition());
var alignmentWithNonMappingEnds = new BamAlignment()
{
Position = 500,
CigarData = new CigarAlignment("5M5I")
};
Assert.Equal(504, alignmentWithNonMappingEnds.GetEndPosition());
alignmentWithNonMappingEnds = new BamAlignment()
{
Position = 500,
CigarData = new CigarAlignment("3S5M5I3S")
};
Assert.Equal(504, alignmentWithNonMappingEnds.GetEndPosition());
alignmentWithNonMappingEnds = new BamAlignment()
{
Position = 500,
CigarData = new CigarAlignment("3S5M3S")
};
Assert.Equal(504, alignmentWithNonMappingEnds.GetEndPosition());
alignmentWithNonMappingEnds = new BamAlignment()
{
Position = 500,
CigarData = new CigarAlignment("3S3M2D3S")
};
Assert.Equal(504, alignmentWithNonMappingEnds.GetEndPosition());
}
public void GetEndPosition_Tests()
{
var alignment1 = new BamAlignment()
{
Position = 500,
CigarData = new CigarAlignment("5M7I19M3D")
};
Assert.Equal(527, alignment1.GetEndPosition());
var alignment2 = new BamAlignment()
{
Position = 500,
CigarData = new CigarAlignment("3I")
};
Assert.Equal(500, alignment2.GetEndPosition());
}
/// <summary>
/// Adds an offset to a specific reference sequence in the index
/// </summary>
private static void AddOffset(ref List<ulong> offsets, ref BamAlignment al, ulong offset)
{
int beg = al.Position >> BamLidxShift;
int end = (al.GetEndPosition() - 1) >> BamLidxShift;
// initialize additional entries if needed
while (offsets.Count < (end + 1)) offsets.Add(0);
if (beg == end)
{
if (offsets[beg] == 0) offsets[beg] = offset;
}
else
{
for (int i = beg; i <= end; i++)
{
if (offsets[i] == 0) offsets[i] = offset;
}
}
}
/// <summary>
/// returns true if the alignment overlaps with the specified interval
/// </summary>
private bool IsOverlap(int begin, int end, BamAlignment alignment)
{
int alignmentBegin = alignment.Position;
int alignmentEnd = alignment.GetEndPosition();
return (alignmentEnd >= begin) && (alignmentBegin < end);
}
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);
}