void ClipReference(HaplotypeSet & reference,
StringArray & refMarkerList,
StringIntHash & referenceHash,
StringArray & markerList,
String & start, String & stop)
{
if (start == "start") start.Clear();
if (stop == "stop") stop.Clear();
// If no clipping was requested, then nothing to do
if (start.IsEmpty() && stop.IsEmpty())
return;
// Find the stretch of target that overlaps with reference
int firstMatch = reference.markerCount, lastMatch = -1;
bool matchStart = false, matchStop = false;
String newStart, newStop;
// First we find overlapping markers in target and, at the same time,
// keep track of the marker nearest suggested start and stop positions
// that overlaps with reference.
for (int i = 0; i < markerList.Length(); i++)
{
String trimmed = markerList[i].Trim();
if (start == trimmed) matchStart = true;
if (stop == trimmed) matchStop = true;
int index = referenceHash.Integer(trimmed);
if (index < 0) continue;
if (index < firstMatch) firstMatch = index;
if (index > lastMatch) lastMatch = index;
if (matchStart)
{
newStart = trimmed;
matchStart = false;
}
if (matchStop)
{
newStop = trimmed;
matchStop = false;
}
}
// If start and stop are not in the reference, adjust them
// according to information in the target list
int startIndex = referenceHash.Integer(start);
int stopIndex = referenceHash.Integer(stop);
if (startIndex < 0 && !start.IsEmpty())
{
if (newStart.IsEmpty()) return;
start = newStart;
startIndex = referenceHash.Integer(start);
}
firstMatch = firstMatch < startIndex ? firstMatch : startIndex;
if (stopIndex < 0 && !stop.IsEmpty())
{
if (newStop.IsEmpty()) return;
stop = newStop;
stopIndex = referenceHash.Integer(stop);
}
lastMatch = lastMatch > stopIndex ? lastMatch : stopIndex;
int clipFrom = !start.IsEmpty() ? firstMatch : 0;
int clipTo = !stop.IsEmpty() ? lastMatch : reference.markerCount - 1;
if (clipFrom > 0 || clipTo < reference.markerCount - 1)
{
printf(" Clipping reference haplotypes to match target ...\n");
reference.ClipHaplotypes(clipFrom, clipTo);
StringArray newMarkerList;
newMarkerList.Dimension(reference.markerCount);
for (int i = clipFrom; i <= clipTo; i++)
newMarkerList[i - clipFrom].Swap(refMarkerList[i]);
newMarkerList.Swap(refMarkerList);
referenceHash.Clear();
for (int i = 0; i < refMarkerList.Length(); i++)
referenceHash.Add(refMarkerList[i].Trim(), i);
printf(" %d Markers Remain After Clipping ...\n", reference.markerCount);
}
}
