private static void AddIntervals(IAnnotatedPosition annotatedPosition,
IIntervalSearch <ISupplementaryInterval> intervalArray, int begin, int end)
{
var intervals = intervalArray.GetAllOverlappingValues(begin, end);
if (intervals == null)
{
return;
}
foreach (var overlappingInterval in intervals)
{
var reciprocalOverlap = annotatedPosition.Position.Start >= annotatedPosition.Position.End
? null
: overlappingInterval.GetReciprocalOverlap(annotatedPosition.AnnotatedVariants[0].Variant);
annotatedPosition.SupplementaryIntervals.Add(
new AnnotatedSupplementaryInterval(overlappingInterval, reciprocalOverlap));
}
}
/// <summary>
/// decompresses the 2-bit notation into bases
/// </summary>
public string Substring(int offset, int length)
{
offset -= _sequenceOffset;
// handle negative offsets and lengths
if (offset < 0 || length < 1 || offset >= NumBases)
{
return(null);
}
// sanity check: avoid going past the end of the sequence
if (offset + length > NumBases)
{
length = NumBases - offset;
}
// allocate more memory if needed
var decompressBuffer = new char[length];
// set the initial state of the buffer
var indexAndShiftTuple = GetBaseIndexAndShift(offset - 1);
int bufferIndex = indexAndShiftTuple.Item1;
int bufferShift = indexAndShiftTuple.Item2;
byte currentBufferSeed = _buffer[bufferIndex];
// get the overlapping masked interval
var maskedIntervals = new List <MaskedEntry>();
_maskedIntervalSearch.GetAllOverlappingValues(offset, offset + length - 1, maskedIntervals);
// get the first masked interval
int numIntervals = maskedIntervals.Count;
bool hasMaskedIntervals = numIntervals > 0;
int currentOffset = 0;
var currentInterval = hasMaskedIntervals ? maskedIntervals[0] : null;
for (int baseIndex = 0; baseIndex < length; baseIndex++)
{
int currentPosition = offset + baseIndex;
if (hasMaskedIntervals && currentPosition >= currentInterval.Begin && currentPosition <= currentInterval.End)
{
// evaluate the masked bases
for (; baseIndex <= currentInterval.End - offset && baseIndex < length; baseIndex++)
{
decompressBuffer[baseIndex] = 'N';
}
baseIndex--;
indexAndShiftTuple = GetBaseIndexAndShift(offset + baseIndex);
bufferIndex = indexAndShiftTuple.Item1;
bufferShift = indexAndShiftTuple.Item2;
currentBufferSeed = _buffer[bufferIndex];
currentOffset++;
hasMaskedIntervals = currentOffset < numIntervals;
currentInterval = hasMaskedIntervals ? maskedIntervals[currentOffset] : null;
}
else
{
// evaluate normal bases
decompressBuffer[baseIndex] = _convertNumberToBase[(currentBufferSeed >> bufferShift) & 3];
bufferShift -= 2;
if (bufferShift < 0)
{
bufferShift = CompressedSequenceReader.MaxShift;
bufferIndex++;
currentBufferSeed = _buffer[bufferIndex];
}
}
}
return(new string(decompressBuffer, 0, length));
}
public string Substring(int offset, int length)
{
offset -= _sequenceOffset;
// handle negative offsets and lengths
if (offset < 0 || length < 1 || offset >= Length)
{
return(null);
}
// sanity check: avoid going past the end of the sequence
if (offset + length > Length)
{
length = Length - offset;
}
// allocate more memory if needed
if (length > _decompressBuffer.Length)
{
_decompressBuffer = new char[length];
}
// set the initial state of the buffer
(int bufferIndex, int bufferShift) = GetBaseIndexAndShift(offset - 1);
byte currentBufferSeed = _buffer[bufferIndex];
// get the overlapping masked interval
var maskedIntervals = _maskedIntervalSearch.GetAllOverlappingValues(offset, offset + length - 1);
// get the first masked interval
var currentOffset = 0;
bool hasMaskedIntervals = maskedIntervals != null;
int numIntervals = maskedIntervals?.Length ?? 0;
var currentInterval = hasMaskedIntervals ? maskedIntervals[0] : null;
for (var baseIndex = 0; baseIndex < length; baseIndex++)
{
int currentPosition = offset + baseIndex;
if (hasMaskedIntervals && currentPosition >= currentInterval.Begin && currentPosition <= currentInterval.End)
{
int numMaskedBases = MaskBases(offset, length, baseIndex, currentInterval);
baseIndex += numMaskedBases - 1;
(bufferIndex, bufferShift) = GetBaseIndexAndShift(offset + baseIndex);
currentBufferSeed = _buffer[bufferIndex];
currentOffset++;
hasMaskedIntervals = currentOffset < numIntervals;
currentInterval = hasMaskedIntervals ? maskedIntervals[currentOffset] : null;
continue;
}
// evaluate normal bases
_decompressBuffer[baseIndex] = _convertNumberToBase[(currentBufferSeed >> bufferShift) & 3];
bufferShift -= 2;
if (bufferShift < 0)
{
bufferShift = CompressedSequenceReader.MaxShift;
bufferIndex++;
currentBufferSeed = _buffer[bufferIndex];
}
}
return(new string(_decompressBuffer, 0, length));
}
