private void ApplyRnaEdits(StringBuilder sb)
{
if (_rnaEdits == null)
{
return;
}
var codingStart = _codingRegion.CdnaStart;
var editOffset = 0;
RnaEditUtilities.SetTypesAndSort(_rnaEdits);
foreach (var rnaEdit in _rnaEdits)
{
//if the edits are in utr regions, we can skip them
var cdsEditStart = rnaEdit.Start - codingStart + editOffset;
if (sb.Length <= cdsEditStart)
{
continue;
}
switch (rnaEdit.Type)
{
case VariantType.SNV:
if (cdsEditStart >= 0)
{
sb[cdsEditStart] = rnaEdit.Bases[0];
}
break;
case VariantType.MNV:
for (var i = 0; i < rnaEdit.Bases.Length && cdsEditStart >= 0; i++)
{
sb[cdsEditStart + i] = rnaEdit.Bases[i];
}
break;
case VariantType.insertion:
if (cdsEditStart >= 0)
{
sb.Insert(cdsEditStart, rnaEdit.Bases);
}
editOffset += rnaEdit.Bases.Length; //account for inserted bases
break;
case VariantType.deletion:
//from the transcripts NM_033089.6 and NM_001317107.1, it seems that deletion edits are
//already accounted for in the exons. So, we don't need to delete any more.
editOffset -= rnaEdit.End - rnaEdit.Start + 1; //account for deleted bases
break;
default:
throw new UserErrorException("Encountered unknown rnaEdit type:" + rnaEdit.Type);
}
}
}
private void ApplyRnaEdits(StringBuilder sb)
{
if (_rnaEdits == null)
{
return;
}
var editOffset = 0;
RnaEditUtilities.SetTypesAndSort(_rnaEdits);
foreach (var rnaEdit in _rnaEdits)
{
int cdnaEditStart = rnaEdit.Start - 1 + editOffset;
switch (rnaEdit.Type)
{
case VariantType.SNV:
if (cdnaEditStart >= 0)
{
sb[cdnaEditStart] = rnaEdit.Bases[0];
}
break;
case VariantType.MNV:
for (var i = 0; i < rnaEdit.Bases.Length && cdnaEditStart >= 0; i++)
{
sb[cdnaEditStart + i] = rnaEdit.Bases[i];
}
break;
case VariantType.insertion:
if (cdnaEditStart >= 0)
{
sb.Insert(cdnaEditStart, rnaEdit.Bases);
}
editOffset += rnaEdit.Bases.Length;
break;
case VariantType.deletion:
editOffset -= rnaEdit.End - rnaEdit.Start + 1;
break;
default:
throw new UserErrorException("Encountered unknown rnaEdit type:" + rnaEdit.Type);
}
}
}
public void RnaEditTypes(int start, int end, string bases, VariantType expectedType)
{
var rnaEdit = new RnaEdit(start, end, bases);
Assert.Equal(expectedType, RnaEditUtilities.GetRnaEditType(rnaEdit));
}
