public ReadCoverageSummary GetCoverageSummary()
{
return(new ReadCoverageSummary()
{
ClipAdjustedStartPosition = ClipAdjustedPosition,
ClipAdjustedEndPosition = ClipAdjustedEndPosition,
Cigar = CigarData.DeepCopy(),
DirectionInfo = GetDirectionInfo()
});
}
/// <summary>
/// This method takes in indexes in the "sequenced read" coordinate system and remaps them to indexes in the
/// "extended read" coordinate system. The mapping between the two coordinate systems is determined by the cigar string.
/// We output the expandedBaseDirectionMap as a by-product of the method, for any downstream consuptions.
/// For helpful examples of what this means, pls check the unit tests.
/// </summary>
/// <param name="indexesInSequencedReadToRemap">An array of indexes in the sequeced read. Ie, if the read is ACXXGT, the sequenced indexes are 01XX23</param>
/// <param name="expandedBaseDirectionMap">An array of the directions for each base (including deletions). Ie, if the read is ACXXGT, the directions might be FFSSRR</param>
/// <returns>indexesInExtendedReadCoordinates</returns>
public int[] SequencedIndexesToExpandedIndexes(int[] indexesInSequencedReadToRemap)
{
var expandedBaseCigarOpMap = CigarData.Expand();
var numIndexesToRemap = indexesInSequencedReadToRemap.Length;
var remappedIndexes = new int[numIndexesToRemap];
int whichIndex = 0;
int maxSequencedIndex = _bamAlignment.Bases.Length - 1;
int maxExpandedIndex = expandedBaseCigarOpMap.Count - 1;
var indexToRemap = indexesInSequencedReadToRemap[whichIndex];
int sequencedBaseIndex = 0;
while (whichIndex < numIndexesToRemap)
{
for (int extendedIndex = 0; extendedIndex <= maxExpandedIndex; extendedIndex++)
{
if ((indexToRemap < 0) || (indexToRemap > maxSequencedIndex))
{
throw new ArgumentException("Check index arguments for SequencedIndexesToExpandedIndexes method.");
}
var cigarOp = expandedBaseCigarOpMap[extendedIndex];
if (cigarOp.IsReadSpan())
{
if (sequencedBaseIndex == indexToRemap)
{
remappedIndexes[whichIndex] = extendedIndex;
whichIndex++;
if (whichIndex >= numIndexesToRemap)
{
return(remappedIndexes);
}
indexToRemap = indexesInSequencedReadToRemap[whichIndex];
}
sequencedBaseIndex++;
}
}
}
return(remappedIndexes);
}
private void UpdateMapFromCigar()
{
if (CigarData == null || CigarData.Count == 0)
{
return;
}
if (CigarData.GetReadSpan() != PositionMap.Length)
{
throw new Exception(string.Format("Invalid cigar '{0}': does not match length {1} of read", CigarData, ReadLength));
}
if (CigarData.Count == 1 && (CigarData[0].Type == 'I' || CigarData[0].Type == 'D'))
{
throw new Exception(string.Format("Invalid cigar '{0}': indel must have anchor", CigarData));
}
int readIndex = 0;
int referencePosition = Position;
for (var cigarOpIndex = 0; cigarOpIndex < CigarData.Count; cigarOpIndex++)
{
var operation = CigarData[cigarOpIndex];
var readSpan = operation.IsReadSpan();
var refSpan = operation.IsReferenceSpan();
for (var opIndex = 0; opIndex < operation.Length; opIndex++)
{
if (readSpan)
{
PositionMap[readIndex] = refSpan ? referencePosition++ : -1;
readIndex++;
}
else if (refSpan)
{
referencePosition++;
}
}
}
}
