//
// Collect region indices for either all region types, or just a few specific region types.
//
//
int CollectRegionIndices(SMRTSequence &read, RegionTable ®ionTable,
std::vector<int> ®ionIndices, RegionType *regionTypes,
int numRegionTypes) {
int regionLow, regionHigh;
int prevNumRegionIndices = regionIndices.size();
if (FindRegionIndices(read, ®ionTable, regionLow, regionHigh)) {
int i;
for (i = regionLow; i < regionHigh; i++) {
if (regionTypes == NULL) {
regionIndices.push_back(i);
}
else {
int t;
for (t = 0; t < numRegionTypes; t++) {
if (regionTable.GetType(i) == regionTypes[t]) {
regionIndices.push_back(i);
break;
}
}
}
}
}
return regionIndices.size() - prevNumRegionIndices;
}
// General functions.
bool LookupHQRegion(int holeNumber, RegionTable ®ionTable,
int &start, int &end, int &score) {
int regionLowIndex, regionHighIndex;
regionLowIndex = regionHighIndex = 0;
regionTable.LookupRegionsByHoleNumber(holeNumber,
regionLowIndex, regionHighIndex);
bool readHasGoodRegion = true;
int regionIndex = regionLowIndex;
while (regionIndex < regionHighIndex and
regionTable.GetType(regionIndex) != HQRegion) {
regionIndex++;
}
if (regionIndex == regionHighIndex) {
start = end = score = 0;
return false;
}
else {
start = regionTable.GetStart(regionIndex);
end = regionTable.GetEnd(regionIndex);
score = regionTable.GetScore(regionIndex);
return true;
}
}
