CustomizationVariables::CustomizationVariables() : VectorMap<uint8, int16>(1, 1) {
removeAll();
unknown = 1;
setNullValue(0);
keyIndex.removeAll(1, 1);
setInsertPlan(SortedVector<uint8>::NO_DUPLICATE);
}
// for map, -null is a NULL vakue assigned
// when no overlaps are detected.
bool ContextMap::handle_null()
{
if ((_i+1) < _argc) {
setNullValue(_argv[_i + 1]);
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
}
return true;
}
ContextMap::ContextMap()
{
// map requires sorted input
setSortedInput(true);
setLeftJoin(true);
// default to BED score column
setColumn(5);
// default to "sum"
setColumnOperation("sum");
// default to "." as a NULL value
setNullValue('.');
}